On the Calculation of Diffusion Coefficients in Confined Fluids and Interfaces with an Application to the Liquid−Vapor Interface of Water

The mechanisms underlying Li+/Mg2+ separation in ZIF-8 under an electric field from atomistic simulations

In this study, we explore the mass transfer and separation mechanism of Li+ and Mg2+ confined within the flexible nanoporous zeolite imidazolate framework ZIF-8 under the influence of an electric field, employing molecular dynamics simulation. Our results highlight that the electric field accelerates the dehydration process of ions and underscore the critical importance of ZIF-8 framework flexibility in determining the separation selectivity of the ZIF-8 membrane. The electric field is shown to diminish ion hydration in the confined space of ZIF-8, notably disrupting the orientation of water molecules in the first hydration shells of ions, leading to an asymmetrical ionic hydration structure characterized by the uniform alignment of water dipoles. Furthermore, despite the geometrical constraints imposed by the ZIF-8 framework, the electric field significantly enhances ionic mobility. Notably, the less stable hydration shell of Li+ facilitates its rapid, dehydration-induced transit through ZIF-8 nanopores, unlike Mg2+, whose stable hydration shell impedes dehydration. Further investigation into the structural characteristics of the six-ring windows traversed by Li+ and Mg2+ ions reveals distinct mechanisms of passage: for Mg2+ ions, significant window expansion is necessary, while for Li+ ions, the mechanism involves both window expansion and partial dehydration. These findings reveal the profound impact of the electric field and framework flexibility on the separation of Li+ and Mg2+, offering critical insights for the potential application of flexible nanoporous materials in the selective extraction of Li+ from salt-lake brine.

Molecular Density Fluctuations Control Solubility and Diffusion for Confined Aqueous Hydrogen

Hydrogen's contribution to a sustainable energy transformation requires intermittent storage technologies, e.g., underground hydrogen storage (UHS). Toward designing UHS sites, atomistic molecular dynamics (MD) simulations are used here to quantify thermodynamic and transport properties for confined aqueous H2. Slit-shaped pores of width 10 and 20 Å are carved out of kaolinite. Within these pores, water yields pronounced hydration layers. Molecular H2 distributes along these hydration layers, yielding solubilities up to ∼25 times those in the bulk. Hydrogen accumulates near the siloxane surface, where water density fluctuates significantly. On the contrary, a dense hydration layer forms on the gibbsite surface, which is, for the most part, depleted of H2. Although confinement reduces water mobility, the diffusion of aqueous H2 increases as the kaolinite pore width decreases, also a consequence of water density fluctuations. These results relate to H2 permeability in underground hydrogen storage sites.

Electrokinetic properties of NaCl solution via molecular dynamics simulations with scaled-charge electrolytes

Scaling ionic charges has become an alternative to polarizable force fields for representing indirect charge transfer effects in molecular simulations. In our work, we apply molecular dynamics simulations to investigate the properties of NaCl aqueous solutions in homogeneous and confined media. We compare classical integer- and scaled-charge force fields for the ions. In the bulk, we validate the force fields by computing equilibrium and transport properties and comparing them with experimental data. Integer-charge ions overestimate dielectric saturation and ionic association. Both force fields present an excess in ion-ion correlation, which leads to a deviation in the ionic conductivity at higher ionic strengths. Negatively charged quartz is used to simulate the confinement effect. Electrostatic interactions dominate counter-ion adsorption. Full-charge ions have stronger and more defined adsorption planes. We obtain the electroosmotic mobility of the solution by combining the shear plane location from non-equilibrium simulations with the ionic distribution from equilibrium simulations. From the Helmholtz-Smoluchowski equation, the zeta potential and the streaming potential coupling coefficient are computed. From an atomic-scale perspective, our molecular dynamics simulations corroborate the hypothesis of maximum packing of the Stern layer, which results in a stable and non-zero zeta potential at high salinity. The scaled-charge model representation of both properties is in excellent qualitative and quantitative agreement with experimental data. With our work, we demonstrate how useful and precise simple scaled-charge models for electrolytes can be to represent complex systems, such as the electrical double layer.

Organic-solvent ditch overlap in reversed-phase liquid chromatography: A molecular dynamics simulation study in cylindrical 6-12 nm-diameter pores

Mass transport through the mesopore space of a reversed-phase liquid chromatography (RPLC) column depends on the properties of the chromatographic interface, particularly on the extent of the organic-solvent ditch that favors the analyte surface diffusivity. Through molecular dynamics simulations in cylindrical RPLC mesopore models with pore diameters between 6 and 12 nm we systematically trace the evolution of organic-solvent ditch overlap due to spatial confinement in the mesopore space of RPLC columns for small-molecule separations. Each pore model of a silica-based, endcapped, C18-stationary phase is equilibrated with two mobile phases of comparable elution strength, namely 70/30 (v/v) water/acetonitrile and 60/40 (v/v) water/methanol, to consider the influence of the mobile-phase composition on the onset of organic-solvent ditch overlap. The simulations show that, as the pore diameter decreases from 9 to 6 nm, the bonded-phase density extends and compacts towards the pore center, which leads to increased accumulation of organic-solvent excess and thus enhanced organic-solvent diffusivity in the ditch. Because the acetonitrile ditch is more pronounced than the methanol ditch, acetonitrile ditch overlap sets in at less severe spatial confinement than methanol ditch overlap. The pore-averaged methanol and acetonitrile diffusivities are considerably raised by ditch overlap in the 6 nm-diameter pore, but also benefit from the ditch (without overlap) in the 7 to 12 nm-diameter pores, whereby local and pore-averaged effects are generally larger for acetonitrile than methanol.

Impact of interfacial curvature on molecular properties of aqueous interfaces

The curvature of soft interfaces plays a crucial role in determining their mechanical and thermodynamic properties, both at macroscopic and microscopic scales. In the case of air/water interfaces, particular attention has recently focused on water microdroplets, due to their distinctive chemical reactivity. However, the specific impact of curvature on the molecular properties of interfacial water and interfacial reactivity has so far remained elusive. Here, we use molecular dynamics simulations to determine the effect of curvature on a broad range of structural, dynamical, and thermodynamical properties of the interface. For a droplet, a flat interface, and a cavity, we successively examine the structure of the hydrogen-bond network and its relation to vibrational spectroscopy, the dynamics of water translation, rotation, and hydrogen-bond exchanges, and the thermodynamics of ion solvation and ion-pair dissociation. Our simulations show that curvature predominantly impacts the hydrogen-bond structure through the fraction of dangling OH groups and the dynamics of interfacial water molecules. In contrast, curvature has a limited effect on solvation and ion-pair dissociation thermodynamics. For water microdroplets, this suggests that the curvature alone cannot fully account for the distinctive reactivity measured in these systems, which are of great importance for catalysis and atmospheric chemistry.

Estimating Position-Dependent and Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories: Existing Methods and Future Outlook

Confinement can substantially alter the physicochemical properties of materials by breaking translational isotropy and rendering all physical properties position-dependent. Molecular dynamics (MD) simulations have proven instrumental in characterizing such spatial heterogeneities and probing the impact of confinement on materials' properties. For static properties, this is a straightforward task and can be achieved via simple spatial binning. Such an approach, however, cannot be readily applied to transport coefficients due to lack of natural extensions of autocorrelations used for their calculation in the bulk. The prime example of this challenge is diffusivity, which, in the bulk, can be readily estimated from the particles' mobility statistics, which satisfy the Fokker-Planck equation. Under confinement, however, such statistics will follow the Smoluchowski equation, which lacks a closed-form analytical solution. This brief review explores the rich history of estimating profiles of the diffusivity tensor from MD simulations and discusses various approximate methods and algorithms developed for this purpose. Besides discussing heuristic extensions of bulk methods, we overview more rigorous algorithms, including kernel-based methods, Bayesian approaches, and operator discretization techniques. Additionally, we outline methods based on applying biasing potentials or imposing constraints on tracer particles. Finally, we discuss approaches that estimate diffusivity from mean first passage time or committor probability profiles, a conceptual framework originally developed in the context of collective variable spaces describing rare events in computational chemistry and biology. In summary, this paper offers a concise survey of diverse approaches for estimating diffusivity from MD trajectories, highlighting challenges and opportunities in this area.

Molecular Insights into Chemical Reactions at Aqueous Aerosol Interfaces

Atmospheric aerosols facilitate reactions between ambient gases and dissolved species. Here, we review our efforts to interrogate the uptake of these gases and the mechanisms of their reactions both theoretically and experimentally. We highlight the fascinating behavior of N2O5 in solutions ranging from pure water to complex mixtures, chosen because its aerosol-mediated reactions significantly impact global ozone, hydroxyl, and methane concentrations. As a hydrophobic, weakly soluble, and highly reactive species, N2O5 is a sensitive probe of the chemical and physical properties of aerosol interfaces. We employ contemporary theory to disentangle the fate of N2O5 as it approaches pure and salty water, starting with adsorption and ending with hydrolysis to HNO3, chlorination to ClNO2, or evaporation. Flow reactor and gas-liquid scattering experiments probe even greater complexity as added ions, organic molecules, and surfactants alter the interfacial composition and reaction rates. Together, we reveal a new perspective on multiphase chemistry in the atmosphere.

On the Statistical Mechanics of Mass Accommodation at Liquid-Vapor Interfaces

We propose a framework for describing the dynamics associated with the adsorption of small molecules to liquid-vapor interfaces using an intermediate resolution between traditional continuum theories that are bereft of molecular detail and molecular dynamics simulations that are replete with them. In particular, we develop an effective single particle equation of motion capable of describing the physical processes that determine thermal and mass accommodation probabilities. The effective equation is parametrized with quantities that vary through space away from the liquid-vapor interface. Of particular importance in describing the early time dynamics is the spatially dependent friction, for which we propose a numerical scheme to evaluate from molecular simulation. Taken together with potentials of mean force computable with importance sampling methods, we illustrate how to compute the mass accommodation coefficient and residence time distribution. Throughout, we highlight the case of ozone adsorption in aqueous solutions and its dependence on electrolyte composition.

Effect of ionic groups on the morphology and transport properties in a novel perfluorinated ionomer containing sulfonic and phosphonic acid groups: a molecular dynamics study

Combining the phosphonic acid group with the sulfonic acid group in PEMs has been shown to be an effective strategy for improving the fuel cell performance. However, the interplay of two different ionic groups and the resulting effect on the membrane properties have not been fully elucidated. Here, we used classical molecular dynamics simulation to investigate the morphologies, transport properties and effects of ionic groups in a novel perfluorinated PEM containing two ionic groups (PFSA-PFPA) in comparison to the corresponding homopolymers. Phase separations between hydrophilic and hydrophobic domains are confirmed in these PEMs and result from the evolution of water clusters formed around the ionic groups. The combination of both ionic groups brings a complicated morphological feature in PFSA-PFPA, with near-cylindrical aqueous domains of large length scales interconnected by tortuous domains of small sizes. And we found that the self-diffusion coefficients of water molecules are strongly related to morphologies, with the water transport in PFSA-PFPA lying between two analogous homopolymers. At the molecular level, we found that the sulfonic and phosphonic acid groups have distinct effects on the coordination behaviors and the dynamics of water molecules and hydronium ions. Strong electrostatic interactions lead to compact coordination structures and sluggish dynamics of hydronium ions around phosphonic acid groups, which determine the morphological evolution and transport properties in PFSA-PFPA. Our study affords insights into the relationship between molecular characteristics and transport properties bridged by phase-separated morphologies in a novel PEM containing both sulfonic acid and phosphonic acid groups, which deepens the understanding of the interplay between two ionic groups and may inspire the rational design of high-performance PEMs.

Ionic Pairing and Selective Solvation of Butylmethylimidazolium Chloride Ion Pairs in DMSO-Water Mixtures: A Comprehensive Examination via Molecular Dynamics Simulations and Potentials of Mean Force Analysis

Ionic liquids (ILs) with dimethyl sulfoxide (DMSO) and water act as a promising solvent medium for the dissolution of cellulose in an efficient manner. To develop a proper solvent system, it is really important to understand the thermodynamics of the molecular solutions consisting of ILs, DMSO, and water. The ion-pairing propensity of the ILs in the presence of DMSO and water plays a crucial role in governing the property of the solvent mixtures. Employing all-atom molecular dynamics simulations, we estimate the potentials of mean force between BMIM+ and Cl- ions in DMSO-water mixtures. Analysis reveals a significant increase in the thermodynamic stability of both contact ion pair (CIP) and solvent-assisted ion pair (SAIP) states with a rising DMSO mole fraction. Thermodynamic assessments highlight the entropic stabilization of CIP states and SAIP states in pure water, in DMSO-water mixtures, and in pure DMSO. The structural analysis reveals that in comparison to the DMSO local density, the local water density is relatively very high around ion pairs, more specifically in the solvation shell of a chloride ion. Preferential binding coefficients also consistently indicate exclusion of DMSO from the ion pair in DMSO-water mixtures. To enhance our understanding regarding the solvent molecules kinetics around the ion pairs, the survival probabilities of DMSO and water are computed. The calculations reveal that the water molecules prefer a prolonged stay in the solvation shell of Cl- ions.

The sensitive aspects of modelling polymer-ceramic composite solid-state electrolytes using molecular dynamics simulations

Solid-state composite electrolytes have arisen as one of the most promising materials classes for next-generation Li-ion battery technology. These composites mix ceramic and solid-polymer ion conductors with the aim of combining the advantages of each material. The ion-transport mechanisms within such materials, however, remain elusive. This knowledge gap can to a large part be attributed to difficulties in studying processes at the ceramic-polymer interface, which are expected to play a major role in the overall ion transport through the electrolyte. Computational efforts have the potential of providing significant insight into these processes. One of the main challenges to overcome is then to understand how a sufficiently robust model can be constructed in order to provide reliable results. To this end, a series of molecular dynamics simulations are here carried out with a variation of certain structural (surface termination and polymer length) and pair potential (van der Waals parameters and partial charges) models of the Li7La3Zr2O12 (LLZO) poly(ethylene oxide) (PEO) system, in order to test how sensitive the outcome is to each variation. The study shows that the static and dynamic properties of Li-ion are significantly affected by van der Waals parameters as well as the surface terminations, while the thickness of the interfacial region - where the structure-dynamic properties are different as compared to the bulk-like regime - is the same irrespective of the simulation setup.

Water/organic liquid interface properties with amine, carboxyl, thiol, and methyl terminal groups as seen from MD simulations

Molecular dynamics simulations were performed to study structural and dynamic properties of polar butanamine/water/butanamine, pentanoic acid/water/pentanoic acid, butanethiol/water/butanethiol, and nonpolar pentane/water/pentane systems. The mass density profiles along the interface normal to the organic liquid/water system, the difference in the local structure of H2 O molecules in bulk and in the vicinity of interface, as well as the diffusion behavior of water molecules at the interface with above-mentioned organic liquids have been investigated. Our MD simulation has shown that the diffusion of water molecules across the water/organic liquid interface is influenced by the hydrogen bondsn HB between water molecules and the terminal groups of organic liquids. It was found that the loss of the hydrogen bondsn HB in the nonpolar organic liquid leads to a decrease in the value of the normal component of the diffusion coefficientD z , while the tangential diffusion coefficients, bothD x andD y , increase.

Structure and Dynamics of Confined Water Inside Diphenylalanine Peptide Nanotubes

Diphenylalanine (FF) peptides exhibit a unique ability to self-assemble into nanotubes with confined water molecules playing pivotal roles in their structure and function. This study investigates the structure and dynamics of diphenylalanine peptide nanotubes (FFPNTs) using all-atom molecular dynamics (MD) and grand canonical Monte Carlo combined with MD (GCMC/MD) simulations with both the CHARMM additive and Drude polarizable force fields. The occupancy and dynamics of confined water molecules were also examined. It was found that less than 2 confined water molecules per FF help stabilize the FFPNTs on the x-y plane. Analyses of the kinetics of confined water molecules revealed distinctive transport behaviors for bound and free water, and their respective diffusion coefficients were compared. Our results validate the importance of polarizable force field models in studying peptide nanotubes and provide insights into our understanding of nanoconfined water.

Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories

Confinement breaks translational and rotational symmetry in materials and makes all physical properties functions of position. Such spatial variations are key to modulating material properties at the nanoscale, and characterizing them accurately is therefore an intense area of research in the molecular simulations community. This is relatively easy to accomplish for basic mechanical observables. Determining spatial profiles of transport properties, such as diffusivity, is, however, much more challenging, as it requires calculating position-dependent autocorrelations of mechanical observables. In our previous paper (Domingues, T.S.; Coifman, R.; Haji-Akbari, A. J. Phys. Chem. B 2023, 127, 5273 10.1021/acs.jpcb.3c00670), we analytically derive and numerically validate a set of filtered covariance estimators (FCEs) for quantifying spatial variations of the diffusivity tensor from stochastic trajectories. In this work, we adapt these estimators to extract diffusivity profiles from MD trajectories and validate them by applying them to a Lennard-Jones fluid within a slit pore. We find our MD-adapted estimator to exhibit the same qualitative features as its stochastic counterpart, as it accurately estimates the lateral diffusivity across the pore while systematically underestimating the normal diffusivity close to hard boundaries. We introduce a conceptually simple and numerically efficient correction scheme based on simulated annealing and diffusion maps to resolve the latter artifact and obtain normal diffusivity profiles that are consistent with the self-part of the van Hove correlation functions. Our findings demonstrate the potential of this MD-adapted estimator in accurately characterizing spatial variations of diffusivity in confined materials.

Phase State, Surface Tension, Water Activity, and Accommodation Coefficient of Water-Organic Clusters Near the Critical Size for Atmospheric New Particle Formation

Interactions between water and organic molecules in sub-4 nm clusters play a significant role in the formation and growth of secondary organic aerosol (SOA) particles. However, a complete understanding of the relevant water microphysics has not yet been achieved due to challenges in the experimental characterization of soft nuclei. Here, we use molecular dynamics simulations to study the phase-mixing states, surface tension, water activity, and water accommodation coefficient of organic-water clusters representative of freshly nucleated SOA particles. Our results reveal large deviations from the behavior expected based on continuum theories. In particular, the phase-mixing state has a strong dependence on cluster size; surface tension displays a minimum at a specific organic-water mass ratio (morg/mw ∼ 4.5 in this study) corresponding to a minimum inhibition of droplet nucleation associated with the Kelvin effect; and the water accommodation coefficient increases by a factor of 2 with nanocluster hygroscopic growth, in agreement with recent experimental studies. Overall, our results yield parametric relations for water microphysical properties in sub-4 nm clusters and provide insight into the role of water in the initial stages of SOA nucleation and growth.

Role of Terminal Groups of cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber

The terminal structures of cis-1,4-polyisoprene (PI) chains play a vital role in the excellent comprehensive performance of Hevea natural rubber (NR) with properties such as high toughness, tear-resistance, and wet skid resistance. The cis-1,4-polyisoprene chain constituting NR exhibits a distinct composition of terminal groups comprising two distinct types, namely, the ω and α terminal groups. The structures of the ω terminal [dimethyl allyl (DMA)-(trans-1,4-isoprene)2] and six kinds of α end groups of the polymer chain of NR have been explored by utilizing a newly developed 2D NMR method. In the present work, we examine different kinds of PI melt systems, and we choose various combinations of terminal groups: Hydrogen, one DMA unit with two trans isoprene units as ω end groups and ester-terminated isopentene (α1), hydroxy-terminated isopentene (α2), ester-terminated isobutane (α3), hydroxy-terminated isobutane (α4), ester-terminated 1,4-cis-isoprene (α5), and hydroxy-terminated 1,4-cis-isoprene (α6), i.e., HPIH (PI0)-pure PI (Hydrogen terminal), ωPIα1 (PII), ωPIα2 (PIII), ωPIα3 (PIIII), ωPIα4 (PIIV), ωPIα5 (PIV), and ωPIα6 (PIVI). We evaluated dynamic and static properties of PI chains such as the end-to-end vector autocorrelation function (C(t)), its average relaxation time (τ), end-to-end distance (Ree), and radius of gyration (Rg). We also estimated the diffusion coefficients of polyisoprene chains and pair correlation functions [radial distribution functions (RDFs)], potentials of mean force (PMFs) in between end residues, and survival probability (P(τ)) of end groups around the end group by analyzing the equilibrated trajectories of full-atom MD simulations. As per the examination of C(t), rotational relaxation time τ, and RDFs, we discovered that the existence of a strong hydrogen bond in α2-α2, α4-α4, and α6-α6 residues makes the dynamics of hydroxy-terminated polyisoprene chains in ωPIα2,α4,α6 melt systems slower. From the analyses of RDFs and PMFs (W(r)), the association between [α2]-[α2], [α4]-[α4], and [α6]-[α6] terminals in ωPIα2,α4,α6 melt systems is significantly stronger than in [ISO]-[ISO] [Hydrogen terminated 1,4-cis-isoprene:(ISO)] in HPIH and ω-ω, [α1]-[α1], [α3]-[α3], and [α5]-[α5] in ωPIα1,α3,α5 systems. We quantified the fraction of cluster formation of terminal groups of a given size in the seven PI melt systems by employing the criteria of PMFs. It is revealed that no stable cluster exists in the HPIH, ωPIα1, ωPIα3, and ωPIα5 melt systems. Conversely, in the ωPIα2, ωPIα4, and ωPIα6 systems, we perceived stable clusters of [(α2)p] [(α4)p] and [(α6)p] end groups where p (2 ≤ x ≤ 6). These stable clusters validate the presence of physical junction points in between hydroxy-terminated polyisoprene chains through their α2, α4, and α6 terminals. These physical junction points might be crucial for superior properties of NR such as high toughness, crack growth resistance, and strain-induced crystallization.

Diffusion and Gas Flow Dynamics in Partially Saturated Smectites

Clays and clay rocks are considered good natural and engineered barriers for deep geological disposal of nuclear waste worldwide. Metal corrosion and organic waste degradation in underground repositories generate significant amounts of gas that should be able to migrate through the multibarrier system to avoid potential pressure buildup, which could be compromising the integrity of the barriers and host rocks. The gas is expected to accumulate in larger pores and eventually form an interconnected network. Under such conditions, the migration of gas molecules takes place both in pore water films and gas-filled macropores. Therefore, mass fluxes depend on the distribution of gas molecules between the water-rich and gas-rich phases and their mobility in both compartments. Classical molecular dynamics (MD) simulations were employed to investigate the mobilities of He, H₂, CO₂, Ar, and CH₄ in a Na-montmorillonite mesopore as a function of the degree of saturation, as well as evaluate the hydrodynamic behavior of the pore fluid in partially saturated clays. The diffusivity of the gas molecules was determined by observing the asymptotic behavior of the mean square displacement in the gas-rich phase and at the gas-water interface. The partition coefficient and Gibbs free energy were analyzed to investigate the transfer of gas molecules between the gas-rich and water-rich phases by observing the molecular trajectories as they cross the vapor-liquid interface. The results revealed that the diffusion coefficient in the gas phase increased with increasing gas-filled pore width and converged asymptotically toward the diffusion coefficient in the bulk state. It could be shown that the diffusion coefficient of gas molecules dissolved in the water films remained constant as long as the interacting water surface was in the bulk-liquid-like phase. This behavior changes in very thin water films. It was observed that the partitioning coefficient of gas molecules at the solid-liquid interface is nearly the same as that in the bulk-liquid-like phase. Partitioning is observed to be strongly dependent on the temperature and gas molecular weights. In the second part of the study, nonequilibrium molecular dynamics (NEMD) simulations were performed to investigate the mobility of gases in pressure-driven decoupled gas-phase dynamics (DGPD) and coupled gas and water phase dynamics (CGWPD) in a partially saturated Na-montmorillonite slit mesopore. The dynamic viscosity of the gas phase was calculated from NEMD simulations and indicated that the viscosity of the gas phase was almost the same in both methods (DGPD and CGWPD). The average slip length for gas molecules at the gas-water interface was also calculated, revealing that the slip-free boundary condition assumed in continuum models is generally invalid for microfluidics and that a slip boundary condition exists at the microscale for specific surface interactions. Finally, a Bosanquet-type equation was developed to predict the diffusion coefficient and dynamic viscosity of gas as a function of the average pore width, gas mean-free path, geometric factor, and thickness of the adsorbed water film.

Thermo-Osmosis in Charged Nanochannels: Effects of Surface Charge and Ionic Strength

Thermo-osmosis refers to fluid migration due to the temperature gradient. The mechanistic understanding of thermo-osmosis in charged nano-porous media is still incomplete, while it is important for several environmental and energy applications, such as low-grade waste heat recovery, wastewater recovery, fuel cells, and nuclear waste storage. This paper presents results from a series of molecular dynamics simulations of thermo-osmosis in charged silica nanochannels that advance the understanding of the phenomenon. Simulations with pure water and water with dissolved NaCl are considered. First, the effect of surface charge on the sign and magnitude of the thermo-osmotic coefficient is quantified. This effect was found to be mainly linked to the structural modifications of an aqueous electrical double layer (EDL) caused by the nanoconfinement and surface charges. In addition, the results illustrate that the surface charges reduce the self-diffusivity and thermo-osmosis of interfacial liquid. The thermo-osmosis was found to change direction when the surface charge density exceeds -0.03C · m^-2. It was found that the thermo-osmotic flow and self-diffusivity increase with the concentration of NaCl. The fluxes of solvent and solute are decoupled by considering the Ludwig-Soret effect of NaCl ions to identify the main mechanisms controlling the behavior. In addition to the advance in microscopic quantification and mechanistic understanding of thermo-osmosis, the work provides approaches to investigate a broader category of coupled heat and mass transfer problems in nanoscale space.

Robust Estimation of Position-Dependent Anisotropic Diffusivity Tensors from Stochastic Trajectories

Materials under confinement can possess properties that deviate considerably from their bulk counterparts. Indeed, confinement makes all physical properties position-dependent and possibly anisotropic, and characterizing such spatial variations and directionality has been an intense area of focus in experimental and computational studies of confined matter. While this task is fairly straightforward for simple mechanical observables, it is far more daunting for transport properties such as diffusivity that can only be estimated from autocorrelations of mechanical observables. For instance, there are well established methods for estimating diffusivity from experimentally observed or computationally generated trajectories in bulk systems. No rigorous generalizations of such methods, however, exist for confined systems. In this work, we present two filtered covariance estimators for computing anisotropic and position-dependent diffusivity tensors and validate them by applying them to stochastic trajectories generated according to known diffusivity profiles. These estimators can accurately capture spatial variations that span over several orders of magnitude and that assume different functional forms. Our kernel-based approach is also very robust to implementation details such as the localization function and time discretization and performs significantly better than estimators that are solely based on local covariance. Moreover, the kernel function does not have to be localized and can instead belong to a dictionary of orthogonal functions. Therefore, the proposed estimator can be readily used to obtain functional estimates of diffusivity rather than a tabulated collection of pointwise estimates. Nonetheless, the susceptibility of the proposed estimators to time discretization is higher at the immediate vicinity of hard boundaries. We demonstrate this heightened susceptibility to be common among all covariance-based estimators.

Confined Electrolytes Show Bulk Dynamics Modulated by Hydrodynamic Couplings with the Walls

We use numerical simulations at the mesoscopic scale, namely, multiparticle collision dynamics (MPCD), to investigate the properties of electrolyte solutions in a charged slit pore. The solution is described within the primitive model of electrolytes, where ions are charged hard spheres embedded in a dielectric medium. Hydrodynamic couplings between ions and with the charged walls are precisely accounted for by the MPCD algorithm. We show that the dynamic properties of ions in this situation strongly differ from the behavior at infinite dilution (ideal case), contrary to what is usually assumed in the usual Poisson-Nernst-Planck description of this kind of systems. As a consequence of confinement, the diffusion coefficients of ions unexpectedly increase with the average ionic density in the systems. This is due to a decrease of the proportion of ions that are slowed down by the wall. Moreover, nonequilibrium simulations are used to estimate the electrical conductivity of these confined electrolytes. We show that the simulation results can be accounted for quantitatively by combining bulk descriptions of the electrical conductivity of electrolytes with a simple description of the hydrodynamics of ions in a slit pore.

Multiple Gas Seepage Mechanisms and Production Development Research for Shale Gas Reservoirs from Experimental Techniques and Theoretical Models

Shale gas seepage theory provides a scientific basis for dynamically analyzing the physical gas flow processes involved in shale gas extraction and for estimating shale gas production. Conventional experimental techniques and theoretical methods applied in seepage research are unable to accurately illustrate shale gas mass transfer processes at the micro- and nanoscale. In view of these scientific issues, the knowledge of seepage mechanisms and production development design was improved from the perspective of experimental techniques and theoretical models in the paper. First, multiple techniques (e.g., focused ion beam scanning electron microscopy and a combination of mercury intrusion porosimetry and adsorption measurement techniques) were integrated to characterize the micro- and nanopore distribution in shales. Then, molecular dynamics simulations were carried out to analyze the microscale distribution of gas molecules in nanopores. In addition, an upscaled gas flow model for the shale matrix was developed based on molecular dynamics simulations. Finally, the coupled flow and productivity models were set up according to a long-term production physical simulation to identify the production patterns for adsorbed and free gas. The research results show that micropores (diameter: <2 nm) and mesopores (diameter: 2-50 nm) account for more than 70% of all the pores in shales and that they are the primary space hosting adsorbed gas. Molecular simulations reveal that microscopic adsorption layers in organic matter nanopores can be as thick as 0.7 nm and that desorption and diffusion are the main mechanisms behind the migration of gas molecules. An apparent permeability model that comprehensively accounts for adsorption, diffusion, and seepage was developed to address the deficiency of Darcy's law in characterizing gas flowability in shale reservoirs. The productivity model results for a certain gas well show that the production in the first three years accounts for more than 50% of its estimated ultimate recovery and that adsorbed gas contributes more to the annual production than free gas in the eighth year. These research results provide theoretical and technical support for improving the theoretical understanding of shale gas seepage and optimizing shale gas extraction techniques in China.

Multiscale modeling of solute diffusion in triblock copolymer membranes

We develop a multiscale simulation model for diffusion of solutes through porous triblock copolymer membranes. The approach combines two techniques: self-consistent field theory (SCFT) to predict the structure of the self-assembled, solvated membrane and on-lattice kinetic Monte Carlo (kMC) simulations to model diffusion of solutes. Solvation is simulated in SCFT by constraining the glassy membrane matrix while relaxing the brush-like membrane pore coating against the solvent. The kMC simulations capture the resulting solute spatial distribution and concentration-dependent local diffusivity in the polymer-coated pores; we parameterize the latter using particle-based simulations. We apply our approach to simulate solute diffusion through nonequilibrium morphologies of a model triblock copolymer, and we correlate diffusivity with structural descriptors of the morphologies. We also compare the model's predictions to alternative approaches based on simple lattice random walks and find our multiscale model to be more robust and systematic to parameterize. Our multiscale modeling approach is general and can be readily extended in the future to other chemistries, morphologies, and models for the local solute diffusivity and interactions with the membrane.

Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles: A Nucleosome-like Model for the Condensed State

Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune "bond" lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol's role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA's conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Overall, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation.

Mobile-Phase Contributions to Organic-Solvent Excess Adsorption and Surface Diffusion in Reversed-Phase Liquid Chromatography

Fast transport of retained analytes in reversed-phase liquid chromatography occurs through surface diffusion in the organic-solvent (OS)-enriched interfacial "ditch" region between the hydrophobic stationary phase and the water (W)-OS mobile phase. Through molecular dynamics simulations that recover the OS excess adsorption isotherms of a typical C₁₈-stationary phase for methanol and acetonitrile, we explore the relation between OS properties, OS excess adsorption, and surface diffusion. The emerging molecular-level picture attributes the mobile-phase contribution to surface diffusion to the hydrogen-bond capability and the eluting power of the OS. The higher affinity of methanol for the formation of W-OS hydrogen bonds at the soft, hydrophobic surface presented by the bonded-phase (C₁₈) chains reduces the OS excess and the related viscosity drop in the ditch. The lower eluting power of methanol, however, translates to increased bonded-phase contacts for analytes, which can increase their mobility gain from surface diffusion above the gain observed with acetonitrile.

Water Network in the Binding Pocket of Fluorinated BPTI-Trypsin Complexes─Insights from Simulation and Experiment

Structural waters in the S1 binding pocket of β-trypsin are critical for the stabilization of the complex of β-trypsin with its inhibitor bovine pancreatic trypsin inhibitor (BPTI). The inhibitor strength of BPTI can be modulated by replacing the critical lysine residue at the P1 position by non-natural amino acids. We study BPTI variants in which the critical Lys15 in BPTI has been replaced by α-aminobutyric acid (Abu) and its fluorinated derivatives monofluoroethylglycine (MfeGly), difluoroethylglycine (DfeGly), and trifluoroethylglycine (TfeGly). We investigate the hypothesis that additional water molecules in the binding pocket can form specific noncovalent interactions with the fluorinated side chains and thereby act as an extension of the inhibitors. We report potentials of mean force (PMF) of the unbinding process for all four complexes and enzyme activity inhibition assays. Additionally, we report the protein crystal structure of the Lys15MfeGly-BPTI-β-trypsin complex (pdb: 7PH1). Both experimental and computational data show a stepwise increase in inhibitor strength with increasing fluorination of the Abu side chain. The PMF additionally shows a minimum for the encounter complex and an intermediate state just before the bound state. In the bound state, the computational analysis of the structure and dynamics of the water molecules in the S1 pocket shows a highly dynamic network of water molecules that does not indicate a rigidification or stabilizing trend in regard to energetic properties that could explain the increase in inhibitor strength. The analysis of the energy and the entropy of the water molecules in the S1 binding pocket using grid inhomogeneous solvation theory confirms this result. Overall, fluorination systematically changes the binding affinity, but the effect cannot be explained by a persistent water network in the binding pocket. Other effects, such as the hydrophobicity of fluorinated amino acids and the stability of the encounter complex as well as the additional minimum in the potential of mean force in the bound state, likely influence the affinity more directly.

Confinement Effects on Distribution and Transport of Neutral Solutes in a Small Hydrophobic Nanopore

Molecular dynamics simulations are used to study confinement effects in small cylindrical silica pores with extended hydrophobic surface functionalization as realized, for example, in reversed-phase liquid chromatography (RPLC) columns. In particular, we use a 6 nm cylindrical and a 10 nm slit pore bearing the same C₁₈ stationary phase to compare the conditions inside the smaller-than-average pores within an RPLC column to column-averaged properties. Two small, neutral, apolar to moderately polar solutes are used to assess the consequences of spatial confinement for typical RPLC analytes with water (W)-acetonitrile (ACN) mobile phases at W/ACN ratios between 70/30 and 10/90 (v/v). The simulated data show that true bulk liquid behavior, as observed over an extended center region in the 10 nm slit pore, is not recovered within the 6 nm cylindrical pore. Instead, the ACN-enriched solvent layer around the C₁₈ chain ends (the ACN ditch), a general feature of hydrophobic interfaces equilibrated with aqueous-organic liquids, extends over the entire pore lumen of the small cylindrical pore. This renders the entire pore a highly hydrophobic environment, where, contrary to column-averaged behavior, neither the local nor the pore-averaged sorption and diffusion of analytes scales directly with the W/ACN ratio of the mobile phase. Additionally, the solute polarity-related discrimination between analytes is enhanced. The consequences of local ACN ditch overlap in RPLC columns are reminiscent of ion transport in porous media with charged surfaces, where electrical double-layer overlap occurring locally in smaller pores leads to discrimination between co- and counterionic species.

Concentration dependent interfacial chemistry of the NaOH(aq): gibbsite interface

Caustic conditions are often employed for dissolution of a wide variety of minerals, where ion sorption, surface diffusion, and interfacial organization impact surface reactivity. In the case of gibbsite, γ-Al(OH)₃, the chemistry at the NaOH_(aq) interface is deeply intertwined with industrial processing of aluminum, including metal production and the disposition of Al-containing wastes. To date, little is known about the structure, speciation, and dynamic behavior of gibbsite interfaces (and that of many other minerals) with NaOH_(aq)-particularly as a function of ionic strength. Yet concentration-dependent interfacial organization and dynamics are a critical starting point to develop a fundamental understanding of the factors that influence dissolution. This work reports equilibrium molecular dynamics simulations of the γ-Al(OH)₃:NaOH_(aq) interface, revealing the sorption behavior and speciation of ions from 0.5-10 M [NaOH]. As inner-sphere complexes, Na⁺ primarily coordinates to the side of the gibbsite hexagonal cavities, while OH^- accepts hydrogen-bonding from the surface-OH groups. The mobility of inner-sphere Na⁺ and OH^- ions is significantly reduced due to a strong surface affinity in comparison to previous reports of NaCl, CaCl₂, or BaCl₂ electrolytes. At high [NaOH], contact ion pairing that is observed in the bulk solution is partially disrupted upon sorption to the gibbsite surface by the individual ion-surface interactions. The molecular-scale changes to surface speciation and competition between ion-surface vs. ion-ion interactions influence surface characterization of gibbsite and potential dissolution processes, providing a valuable baseline for starting conditions needed within future reactive molecular simulations.

Statistical physics of inhomogeneous transport: Unification of diffusion laws and inference from first-passage statistics

Characterization of composite materials, whose properties vary in space over microscopic scales, has become a problem of broad interdisciplinary interest. In particular, estimation of the inhomogeneous transport coefficients, e.g., the diffusion coefficient or the heat conductivity, which shape important processes in biology and engineering, is a challenging task. The analysis of such systems is further complicated because two alternative formulations of the inhomogeneous transport equations exist in the literature-the Smoluchowski and Fokker-Planck equations, which are also related to the so-called Ito-Stratonovich dilemma. Using the theory of statistical physics, we show that the two formulations, usually regarded as distinct models, are physically equivalent. From this result we develop efficient estimates for the transverse space-dependent diffusion coefficient in fluids near a phase boundary. Our method requires only measurements of escape probabilities and mean exit times of molecules leaving a narrow spatial region. We test our estimates in three case studies: (i) a Langevin model of a Büttikker-Landauer ratchet; atomistic molecular-dynamics simulations of liquid-water molecules in contact with (ii) vapor, and (iii) soap (surfactant) film which has promising applications in physical chemistry. Our analysis reveals that near the surfactant monolayer the mobility of water molecules is slowed down almost twice with respect to the bulk liquid. Moreover, the diffusion coefficient of water correlates with the transition from hydrophilic to hydrophobic parts of the film.

Salt Enrichment and Dynamics in the Interface of Supercooled Aqueous Droplets

The interconversion reaction of NaCl between the contact-ion pair (CIP) and the solvent-separated ion pair (SSIP) as well as the free-ion state in cold droplets has not yet been investigated. We report direct computational evidence that the lower is the temperature, the closer to the surface the ion interconversion reaction takes place. In supercooled droplets the enrichment of the subsurface in salt becomes more evident. The stability of the SSIP relative to the CIP increases as the ion-pairing is transferred toward the droplet's outer layers. In the free-ion state, where the ions diffuse independently in the solution, the number density of Cl^- shows a broad maximum in the interior in addition to the well-known maximum in the surface. In the study of the reaction dynamics, we find a weak coupling between the interionic NaCl distance reaction coordinate and the solvent degrees of freedom, which contrasts with the diffusive crossing of the free energy barrier found in bulk solution modeling. The H₂O self-diffusion coefficient is found to be at least an order of magnitude larger than that in the bulk solution. We propose to exploit the enhanced surface ion concentration at low temperature to eliminate salts from droplets in native mass spectrometry ionization methods.

Adsorption characteristics of peptides on ω-functionalized self-assembled monolayers: a molecular dynamics study

Molecular dynamics simulations were employed to investigate the adsorption behavior of a variety of amino-acid side-chain analogs (SCAs) and a β-hairpin (HP7) peptide on a series of liquid-like self-assembled monolayers (SAMs) with terminal functional groups of -OH, -OCH₃, -CH₃, and -CF₃. The relationships between the adsorption free energy of the SCAs and the interfacial properties of water on the SAMs were examined to determine the acute predictors of protein adsorption on the SAM surfaces. The structural changes of HP7 on the SAM surfaces were also investigated to understand the relationship between the surface nature and protein denaturation. It was found that the adsorption free energy of the SCAs was linearly related to the surface hydrophobicity, which was computed as the free energy of cavity formation near the SAM-water interfaces. In addition, the hydrophobic -CH₃ and -CF₃ SAMs produced substantial conformational changes in HP7 because of the strong hydrophobic attractions to the nonpolar side chains. The hydrophilic surface terminated by -OH also promoted structural changes in HP7 resulting from the formation of hydrogen bonds between the hydrophilic tail and HP7. Consequently, the moderate amphiphilic surface terminated by -OCH₃ avoided the denaturation of HP7 most efficiently, thus improving the biocompatibility of the surface. In conclusion, these results provide a deep understanding of protein adsorption for a wide range of polymeric surfaces, and they can potentially aid the design of appropriate biocompatible coatings for medical applications.

New Framework for Computing a General Local Self-Diffusion Coefficient Using Statistical Mechanics

Widely applicable, modified Green-Kubo expressions for the local diffusion coefficient (D_l) are obtained using linear response theory. In contrast to past definitions in use, these expressions are statistical mechanical results. Molecular simulations of systems with anisotropic diffusion and an inhomogeneous density profile confirm the validity of the results. Diffusion coefficients determined from different expressions in terms of currents and velocity correlations agree in the limit of large systems. Furthermore, they apply to arbitrarily small local regions, making them readily applicable to nanoscale and inhomogeneous systems where knowledge of D_l is important.

Dynamics and Surface Propensity of H+ and OH- within Rigid Interfacial Water: Implications for Electrocatalysis

Facile solvent reorganization promoting ion transfer across the solid-liquid interface is considered a prerequisite for efficient electrocatalysis. We provide first-principles insight into this notion by examining water self-ion dynamics at a highly rigid NaCl(100)-water interface. Through extensive density functional theory molecular dynamics simulations, we demonstrate for both acidic and alkaline solutions that Grotthuss dynamics is not impeded by a rigid water structure. Conversely, decreased proton transfer barriers and a striking propensity of H₃O⁺ and OH^- for stationary interfacial water are found. Differences in the ideal hydration structure of the ions, however, distinguish their behavior at the water contact layer. While hydronium can maintain its optimal solvation, the preferentially hypercoordinated hydroxide is repelled from the immediate vicinity of the surface due to interfacial coordination reduction. This has implications for alkaline hydrogen electrosorption in which the formation of undercoordinated OH^- at the surface is proposed to contribute to the observed sluggish kinetics.

Consequences of Cylindrical Pore Geometry for Interfacial Phenomena in Reversed-Phase Liquid Chromatography

The interfacial phenomena behind analyte separation in a reversed-phase liquid chromatography column take place nearly exclusively inside the silica mesopores. Their cylindrical geometry can be expected to shape the properties of the chromatographic interface with consequences for the analyte density distribution and diffusivity. To investigate this topic through molecular dynamics simulations, we introduce a cylindrical pore inside a slit pore configuration, where the inner curved and outer planar silica surface bear the same bonded phase. The present model replicates an average-sized (9 nm) mesopore in an endcapped C₁₈ column equilibrated with a mobile phase of 70/30 (v/v) water/acetonitrile. Simulations performed for ethylbenzene and acetophenone show that the surface curvature shifts the bonded phase and analyte density toward the pore center, decreases the solvent density in the bonded-phase region, increases the acetonitrile excess in the interfacial region, and considerably enhances the surface diffusivity of both analytes. Overall, the cylindrical pore provides a more hydrophobic environment than the slit pore. Ethylbenzene density is decidedly increased in the cylindrical pore, whereas acetophenone density is nearly equally distributed between the cylindrical and slit pore. The cylindrical pore geometry thus sharpens the discrimination between the apolar and moderately polar analytes while enhancing the mass transport of both.

Effect of graphitic anode surface functionalization on the structure and dynamics of electrolytes at the interface

Surface termination on a graphitic surface and the type of electrolytes in lithium-ion batteries (LIBs) play an important part in determining the structure, composition, and thus, the quality of the emergent solid electrolyte interphase. In this paper, we analyze the structure and dynamics of electrolyte molecules in multi-component electrolyte with varying species compositions combinatorially paired with four different graphitic surfaces terminated with hydrogen, hydroxyl, carbonyl, and carboxyl to explore the interplay between surface chemistry and electrolyte dynamics at electrode/electrolyte interfaces. Addition of dimethyl carbonate and fluoroethylene carbonate brought substantial changes in the ethylene carbonate (EC) and LiPF₆ surface population density for hydroxyl and carbonyl surfaces. Strong density oscillation and drastic slowing of the dynamics of the electrolyte molecules at the interface are reported for all the systems. While these observations are universal, carboxyl surfaces have the strongest local and long-range effects. Characterization of the average dipole direction at the interface shows strong orientational preferences of ethylene carbonate molecules. EC molecules are preferred to be oriented either almost parallel or perpendicular to the hydroxyl surface, are tilted between parallel and perpendicular with a higher angle of incidence of the dipole vs surface normal on the carbonyl surface than on the hydroxyl surface, and are oriented perpendicularly against the carboxyl surface. These differences highlight the significant effect of graphite surface termination on the dynamics of the electrolytes and provide insight into the complex interplays between electrolyte species and graphite anode in LIBs.

Edge premelting of two-dimensional ices

The surface of a three-dimensional ice crystal naturally has a quasi-liquid layer (QLL) at temperatures below its bulk melting point, due to a phenomenon called surface premelting. Here, we show that the edges of a two-dimensional (2D) bilayer hexagonal ice adsorbed on solid surfaces undergo premelting as well, resulting in the formation of quasi-liquid bands (QLBs) at the edges. Our extensive molecular dynamics simulations show that the QLB exhibits structure and dynamics indistinguishable from the bilayer liquid phase, acting as a lower-dimensional analog of the QLL on the bulk ice. We further find that at low temperatures, the width of the QLBs at armchair-type edges of the 2D ice is almost identical to that at zigzag-type edges but becomes far greater than the latter at temperatures near the melting point. The chirality-dependent edge premelting of 2D ices should add an important new ingredient to the heterogeneity of premelting.

Unveiling Interfacial Li-Ion Dynamics in Li7La3Zr2O12/PEO(LiTFSI) Composite Polymer-Ceramic Solid Electrolytes for All-Solid-State Lithium Batteries

Unlocking the full potential of solid-state electrolytes (SSEs) is key to enabling safer and more-energy dense technologies than today's Li-ion batteries. In particular, composite materials comprising a conductive, flexible polymer matrix embedding ceramic filler particles are emerging as a good strategy to provide the combination of conductivity and mechanical and chemical stability demanded from SSEs. However, the electrochemical activity of these materials strongly depends on their polymer/ceramic interfacial Li-ion dynamics at the molecular scale, whose fundamental understanding remains elusive. While this interface has been explored for nonconductive ceramic fillers, atomistic modeling of interfaces involving a potentially more promising conductive ceramic filler is still lacking. We address this shortfall by employing molecular dynamics and enhanced Monte Carlo techniques to gain unprecedented insights into the interfacial Li-ion dynamics in a composite polymer-ceramic electrolyte, which integrates polyethylene oxide plus LiN(CF₃SO₂)₂ lithium imide salt (LiTFSI), and Li-ion conductive cubic Li₇La₃Zr₂O₁₂ (LLZO) inclusions. Our simulations automatically produce the interfacial Li-ion distribution assumed in space-charge models and, for the first time, a long-range impact of the garnet surface on the Li-ion diffusivity is unveiled. Based on our calculations and experimental measurements of tensile strength and ionic conductivity, we are able to explain a previously reported drop in conductivity at a critical filler fraction well below the theoretical percolation threshold. Our results pave the way for the computational modeling of other conductive filler/polymer combinations and the rational design of composite SSEs.

Charge State Dependence of Amino Acid Propensity at Water Surface: Mechanisms Elucidated by Molecular Dynamics Simulations

Atmospheric aerosols contain a variety of compounds, among them free amino acids and salt ions. The pH of the aerosol droplets depends on their origin and environment. Consequently, compounds like free amino acids found in the droplets will be at different charge states, since these states to a great extent depend on the surrounding pH condition. In droplets of marine origin, amino acids are believed to drive salt ions to the water surface and a pH-dependent amino acid surface propensity will, therefore, indirectly affect many processes in atmospheric chemistry and physics such as for instance cloud condensation. To understand the surface propensity of glycine, valine, and phenylalanine at acidic, neutral, and basic pH, we used molecular dynamics (MD) simulations to investigate them at three different charge states in water. Their respective surface propensities were obtained by the means of a potential of mean force (PMF) in an umbrella sampling approach. Glycine was found to have no preference for the surface, while both valine and phenylalanine showed high propensities. Among the charge states of the surface-enriched ones, the cation, representing the amino acids at low pH, was found to have the highest affinity. Free energy decomposition revealed that the driving forces depend strongly on the nature of the amino acid and its charge state. In phenylalanine, the main factor was found to be a substantial entropy gain, likely related to the side chain, whereas in valine, hydrogen bonding to the functional groups leads to favorable energies and, in turn, affects the surface propensity. A significant gain in water-water enthalpy was seen for both valine and phenylalanine.

Nanoconfinement between Graphene Walls Suppresses the Near-Wall Diffusion of the Ionic Liquid [BMIM][PF6]

We identify two distinct regimes for the diffusion of the ionic liquid [BMIM][PF₆] confined between parallel graphene walls using molecular dynamics simulations. Within 2 nm of the wall, the cations and anions form a well-defined layered structure. In this region, the in-plane diffusion coefficients are suppressed when compared to their bulk values and increase monotonically with the distance away from the wall. Beyond 2 nm from the wall, the density profile and in-plane diffusion coefficients recover their bulk values. The channel-averaged in-plane diffusion coefficients increase monotonically with wall separation and recover the bulk values at a separation of 15 nm. A simple semianalytical model is proposed that mirrors this trend. The results also highlight the importance of applying a finite-size correction to molecular dynamics-predicted diffusion coefficients of confined liquids, which may otherwise be unusually larger than their bulk values.

Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes

Self-assembling cyclic peptide nanotubes can form nanopores when they are inserted in lipid bilayers, acting as ion and/or water permeable channels. In order to improve the versatility of these systems, it is possible to specifically design cyclic peptides with a combination of natural and non-natural amino acids, enabling the control of the nature of the inner cavity of the channels. Here, the behavior of two types of self-assembling peptide motifs, alternating α-amino acids with γ- or δ-aminocycloalkanecarboxylic acids, is studied via molecular dynamics (MD) simulations. The behavior of water molecules in nanopores is expected to affect the properties of these channels and therefore merits detailed examination. A number of water models commonly used in MD simulations have been validated by how well they reproduce bulk water properties. However, it is less clear how these water models behave in the nanoconfined condition inside a channel. The behavior of four different water models-TIP3P, TIP4P, TIP4P/2005, and OPC-are evaluated in MD simulations of self-assembled cyclic peptide nanotubes of distinct composition and diameter. The dynamic behavior of the water molecules and ions in these designed artificial channels depends subtly on the water model used. TIP3P water molecules move faster than those of TIP4P, TIP4P/2005, and OPC. This demeanor is clearly observed in the filling of the nanotube, in water diffusion within the pore, and in the number and stability of hydrogen bonds of the peptides with water. It was also shown that the water model influences the simulated ion flux through the nanotubes, with TIP3P producing the greatest ion flux. Additionally, the two more recent models, TIP4P/2005 and OPC, which are known to reproduce the experimental self-diffusion coefficient of bulk water quite well, exhibit very similar results under the nanoconfined conditions studied here. Because none of these models have been parametrized specifically for waters confined in peptide nanotubes, this study provides a point of reference for further validation.

Supercooled liquid-like dynamics in water near a fully hydrated titania surface: Decoupling of rotational and translational diffusion

We report an ab initio molecular dynamics (MD) simulation investigating the effect of a fully hydrated surface of TiO₂ on the water dynamics. It is found that the universal relation between the rotational and translational diffusion characteristics of bulk water is broken in the water layers near the surface with the rotational diffusion demonstrating progressive retardation relative to the translational diffusion when approaching the surface. This kind of rotation-translation decoupling has so far only been observed in the supercooled liquids approaching glass transition, and its observation in water at a normal liquid temperature is of conceptual interest. This finding is also of interest for the application-significant studies of the water interaction with fully hydrated nanoparticles. We note that this is the first observation of rotation-translation decoupling in an ab initio MD simulation of water.

Collective Solvation and Transport at Tetrahydrofuran-Silica Interfaces for Separation of Aromatic Compounds: Insight from Molecular Dynamics Simulations

We have performed umbrella sampling molecular dynamics simulations to study the separation mechanism of aromatic compounds at the tetrahydrofuran (THF)-methanol-silica interface by liquid chromatography. Solute molecules with different polarities (naphthol and naphthalene) are selected as representative aromatic compounds. For the polar solute (naphthol), the free energy profile shows a deep minimum near the THF-silica interface, suggesting strong interactions with the polar surface. When methanol is added to the interface, there is a sharp increase in naphthol's free energy minimum, and the corresponding diffusion dynamics also undergoes a dramatic change. These findings explain the fast separation mechanism in recent experiments of separating fused ring compounds in asphaltenes with liquid chromatography. Further solvation structure and orientation analysis suggest that apolar and polar solutes may find their own comfort zones several angstroms away from the interface, and their phenyl ring's orientations would undergo a parallel-to-perpendicular transition as the solute molecule moves away from the surface. Extending our simulation studies to systems with different solute concentrations reveals that there is a decrease in the adsorption free energy accompanied by enhanced surface diffusion as the solute concentration increases, which is related to the crowding in the interfacial layers. Our simulation analysis gives a detailed microscopic description of solute solvation and transport at the THF-silica chromatography interface and will be helpful for improving separation protocols in future applications.

Insights from molecular simulations about dead time markers in reversed-phase liquid chromatography

Among the most popular compounds to estimate the hold-up time in reversed-phase liquid chromatography (RPLC) are acetone and uracil, which are considered as too small and too polar, respectively, for retention by the hydrophobic stationary phase, although their observed elution behavior does not fully support this assumption. We investigate how acetone and uracil as solutes interact with the chromatographic interface through molecular dynamics simulations in an RPLC mesopore model of a silica-supported, endcapped, C₁₈ phase equilibrated with a water (W)‒acetonitrile (ACN) mobile phase. The simulation results provide a molecular-level explanation for the observed elution behavior of acetone and uracil, but also question whether true dead time markers for RPLC exist. Both solutes have a density maximum in the interfacial region in addition to a low presence in the bonded-phase region, but these density peaks clearly differ from the adsorption and partitioning peaks of true analytes. Acetone partially behaves like a co-solvent of ACN and partially like the analyte acetophenone. Like ACN, acetone can be found in the first and second layer of solvent molecules at the silica surface; like acetophenone, acetone adsorbs to the bonded-phase chains by orienting its polar group to the bulk region to sustain hydrogen bonds with W molecules. Uracil behavior is governed by a need for extensive hydrogen-bond coordination by W molecules. Uracil adsorbs to the very edge of the bonded-phase chains, on the bulk-region side of the ACN density maximum in the interfacial region. Further penetration into the chains is prevented by the absence of W molecules, which are not found deeper in the bonded phase, except at the silica surface. Contrary to true analytes, accumulation of uracil and acetone in the interfacial region ceases at an equimolar presence of W and ACN in the mobile phase (at 70‒80% ACN volume fraction). Uracil achieves a closer approximation of the stationary-phase limit than acetone, but carries the risk of HILIC retention at high ACN fraction in the mobile phase.

The role of solute polarity on methanol-silica interfacial solvation: a molecular dynamics study

The solvation structure and dynamics of small organic molecules at the methanol-silica interface are important for understanding the reaction dynamics in heterogeneous catalysis as well as the transport mechanisms in liquid chromatography. The role of solute polarity in interfacial solvation at the methanol-silica interface has been investigated via umbrella sampling molecular dynamics (MD) simulations and 1,3-propanediol and n-pentane were selected as representative species of polar and apolar solutes. Free energy calculations reveal that it took a similar free energy cost to transfer both solute molecules from the interface to the bulk, despite the huge difference in their polarities. The 1,3-propendiol molecule can penetrate the adsorbed methanol layer and form hydrogen bonds with the silica surface with its backbone perpendicular to the silica surface, resulting in a significant slowdown of translational and rotational dynamics. Further analysis of solvent density and solute orientations suggest that at the minimum of the adsorption free energy curve, the 1,3-propanediol molecule is in a desolvated state, while n-pentane is in a solvated state. The collective effect of solute concentration has also been studied by unbiased MD simulations, and the free energy barriers of transferring the solute molecule from the interface to bulk, as well as the parallel diffusion coefficients at the interface, show a non-monotonic dependence on solute concentration, which can be related to the crowded environment in the interfacial layers.