Pytim: A python package for the interfacial analysis of molecular simulations

Computational insight into the effect of alkyl chain length in tetraalkylammonium-based deep eutectic solvents

The effect of the increase in the alkyl chain length of cation on the properties of deep eutectic solvents based on ethylene glycol has been investigated employing classical molecular dynamics simulations. The change in the structural and dynamic properties in both the bulk and liquid-vapor interface is explored through various analyses. The interaction between the anion and the ethylene glycol increases with an increase in the alkyl chain length of the cation, as observed in the increase of the lifetime of the hydrogen bond formed between the two. The terminal carbon atoms are found to be closer to each other when the cation changes from tetraethylammonium to tetrabutylammonium. The cations are located closer to the interface, and the association of the alkyl chains becomes more significant with increased alkyl chain length, decreasing the surface tension values.

Disentangling the molecular polarizability and first hyperpolarizability of methanol-air interfaces

Liquid-air interfaces have extensive implications in different areas of interest because the dynamical processes at the interface can be different from those in bulk. Thus, its characterization, understanding, and control may be pivotal in advancing discoveries. However, characterizing the interface requires special and selective tools to avoid signals from the bulk region. This surface specificity and versatility is achieved by using the second harmonic generation (SHG) responses. This study adopts multiscale simulation methods to evaluate the surface SHG responses of methanol-air interfaces with submonolayer resolution tackled by sequentially using classical molecular dynamics simulations under different temperatures and then employing quantum chemistry methods to compute the molecular first hyperpolarizabilities (β). This approach ensures the configurational diversity required to evaluate the average β values. The main achievements are (i) a quasi-absence of surface sensitivity of the mean polarizability 〈α〉 with values about 2% larger than those obtained in bulk, (ii) conversely, smooth variations on the polarizability anisotropy Δα are observed up to the fourth molecular layer at around 20 Å from the interface, and (iii) narrow interfacial effects on the SHG responses, β(-2ω;ω,ω), which are limited to the first molecular layer (∼3.0 Å) and characterized by a high contrast in the βZZZ(-2ω;ω,ω) tensor component between the first and the subsequent layers. Similar trends are obtained at different temperatures or when increasing the number of methanol molecules treated at the quantum chemistry level, indicating the robustness of the approach for describing the dipolar molecular responses of air-liquid interfaces.

Predicting the Geometry of Core-Shell Structures: How a Shape Changes with Constant Added Thickness

The core-shell assembly motif is ubiquitous in chemistry. While the most obvious examples are core/shell-type nanoparticles, many other examples exist. The shape of the core/shell constructs is poorly understood, making it impossible to separate chemical effects from geometric effects. Here, we create a model for the core/shell construct and develop proof for how the eccentricity is expected to change as a function of the shell. We find that the addition of a constant thickness shell always creates a relatively more spherical shape for all shapes covered by our model unless the shape is already spherical or has some underlying radial symmetry. We apply this work to simulated AOT reverse micelles and demonstrate that it is remarkably successful at explaining the observed shapes of the chemical systems. We identify the three specific cases where the model breaks down and how this impacts eccentricity.

Phase separation of multicomponent peptide mixtures into dehydrated clusters with hydrophilic cores

Phase separation of biomolecules underlies the formation and regulation of various membraneless condensates in cells. How condensates function reliably while surrounded by heterogeneous and dynamic mixtures of biomolecular components with specific and nonspecific interactions is yet to be understood. Studying multicomponent biomolecular mixtures with designer peptides has recently become an attractive avenue for learning about physicochemical principles governing cellular condensates. In this work, we employed long-timescale atomistic simulations of multicomponent tripeptide mixtures with all residue substitutions to illuminate the nature of direct and water-mediated interactions in a prototypical cellular condensate environment. We find that peptide mixtures form clusters with inverse hydrophobic order. Most multivalent and charged residues are localized in the cluster's core, with a large fraction of nonaromatic hydrophobic residues remaining on the surface. This inverse hydrophobic order in peptide clusters is partly driven by the expulsion of nonspecifically bound water molecules following peptide cluster growth. The growth of clusters is also accompanied by the formation of increasing numbers of specific water-mediated interactions between polar and charged residues. While the present study focused on the condensation of short peptide motifs, the general findings and analysis techniques should be helpful for future studies on larger peptides and protein condensation.

Variation of Surface Propensity of Halides with Droplet Size and Temperature: The Planar Interface Limit

The radial number density profiles of halide and alkali ions in aqueous clusters with equimolar radius ≲1.4 nm, which correspond to ≲255 H2O molecules, have been extensively studied by computations. However, the surface abundance of Cl-, Br-, and I- relative to the bulk interior in these smaller clusters may not be representative of the larger systems. Indeed, here we show that the larger the cluster is, the lower the relative surface abundance of chaotropic halides is. In droplets with an equimolar radius of ≈2.45 nm, which corresponds to ≈2000 H2O molecules, the polarizable halides show a clear number density maximum in the droplet's bulk-like interior. A similar pattern is observed in simulations of the aqueous planar interface with halide salts at room temperature. At elevated temperature the surface propensity of Cl- decreases gradually, while that of I- is partially preserved. The change in the chaotropic halide location at higher temperatures than the room temperature may considerably affect photochemical reactivity in atmospheric aerosols, vapor-liquid nucleation and growth mechanisms, and salt crystallization via solvent evaporation. We argue that the commonly used approach of nullifying parameters in a force field in order to find the factors that determine the ion location does not provide transferable insight into other force fields.

Liquid-Vapor Interface of Aqueous Ethylene Glycol Solutions: A Molecular Dynamics Study

While the organic constituent in an aqueous binary solution enriches its liquid-vapor (l-v) interface, the extent of enrichment can depend nonlinearly on its mole fraction. A microscopic quantification and rationalization of this behavior are crucial to understand the dependence of properties such as surface tension and evaporation rate of the solution on its composition. Extensive all-atom molecular dynamics simulations of aqueous ethylene glycol (EG) solutions show that the composition of the solution at the l-v interface deviates the most from that in the bulk solution at an EG mole fraction of 0.3. The population of EG molecules with their central C-C dihedral in the gauche conformation was found to be higher at the l-v interface than that in the bulk solution to facilitate the orientation of its hydrophobic methyl groups toward the vapor phase. Free energy calculations reveal that in dilute EG solutions, an EG molecule is most stable at the l-v interface. The behavior of vapor pressure in aqueous EG solutions is ideal and follows Raoult's law, while in contrast, the aqueous solution of dimethyl sulfoxide does not. A rationale for the same is provided through the orientational distribution of interfacial water molecules in the respective solutions.

Does the Sign of Charge Affect the Surface Affinity of Simple Ions?

The role the charge sign of simple ions plays in determining their surface affinity in aqueous solutions is investigated by computer simulation methods. For this purpose, the free surface of aqueous solutions of fictitious salts is simulated at finite concentration both with nonpolarizable point-charge and polarizable Gaussian-charge potential models. The salts consist of monovalent cations and anions that are, apart from the sign of their charge, identical to each other. In particular, we consider the small Na⁺ and the large I^- ions together with their charge-inverted counterparts. In an attempt to avoid the interference even between the behavior of cations and anions, we also simulate systems containing only one of the above ions, and determine the free energy profile of these ions across the liquid-vapor interface of water at infinite dilution by potential of mean force (PMF) calculations. The obtained results reveal that, in the case of small ions, the anion is hydrated considerably stronger than the cation due to the close approach of water H atoms, bearing a positive fractional charge. As a consequence, the surface affinity of a small anion is even smaller than that of its cationic counterpart. However, considering that small ions are effectively repelled from the water surface, the importance of this difference is negligible. Further, a change in the hydration energy trends of the two oppositely charged ions is observed with their increasing size. This change is largely attributed to the fact that, with increasing ion size, the factor of 2 in the magnitude of the fractional charge of the closely approaching water atoms (i.e., O around cations and H around anions) outweighs the closer approach of the H than the O atom in the hydration energy. Thus, for large ions, being already surface active themselves, the surface affinity of the anion is larger than that of its positively charged counterpart. Further, such a difference is seen even in the case when the sign of the surface potential favors the adsorption of cations.

Microscopic insights on clathrate hydrate growth from non-equilibrium molecular dynamics simulations

Clathrate hydrates form and grow at interfaces. Understanding the relevant molecular processes is crucial for developing hydrate-based technologies. Many computational studies focus on hydrate growth within the aqueous phase using the 'direct coexistence method', which is limited in its ability to investigate hydrate film growth at hydrocarbon-water interfaces. To overcome this shortcoming, a new simulation setup is presented here, which allows us to study the growth of a methane hydrate nucleus in a system where oil-water, hydrate-water, and hydrate-oil interfaces are all simultaneously present, thereby mimicking experimental setups. Using this setup, hydrate growth is studied here under the influence of two additives, a polyvinylcaprolactam oligomer and sodium dodecyl sulfate, at varying concentrations. Our results confirm that hydrate films grow along the oil-water interface, in general agreement with visual experimental observations; growth, albeit slower, also occurs at the hydrate-water interface, the interface most often interrogated via simulations. The results obtained demonstrate that the additives present within curved interfaces control the solubility of methane in the aqueous phase, which correlates with hydrate growth rate. Building on our simulation insights, we suggest that by combining data for the potential of mean force profile for methane transport across the oil-water interface and for the average free energy required to perturb a flat interface, it is possible to predict the performance of additives used to control hydrate growth. These insights could be helpful to achieve optimal methane storage in hydrates, one of many applications which are attracting significant fundamental and applied interests.

Surface Affinity of Tetramethylammonium Iodide in Aqueous Solutions: A Combined Experimental and Computer Simulation Study

The surface affinity of tetramethylammonium iodide (TMAI) in aqueous solutions is investigated by surface tension measurements and molecular dynamics computer simulations. Experiments, performed in the entire composition range of solubility using the pendant drop method with two different setups, clearly reveal that TMAI is a weakly capillary active salt. Computer simulations performed with the AMBER force field reproduce the experimental data very well, while two other major force fields (i.e., CHARMM and OPLS) can still reproduce the experimental trend qualitatively; however, even qualitative reproduction of the experimental trend requires scaling down the ion charges according to the Leontyev-Stuchebrukhov correction. On the other hand, the GROMOS force field fails in reproducing the experimentally confirmed capillary activity of TMAI. Molecular dynamics simulation results show that, among the two ions, iodide has a clearly larger surface affinity than tetramethylammonium (TMA⁺). Further, the adsorption of the I^- anions is strictly limited to the first molecular layer beneath the liquid-vapor interface, which is followed by several layers of their depletion. On the other hand, the net negative charge of the surface layer, caused by the excess amount of I^- with respect to TMA⁺, is compensated by a diffuse layer of adsorbed TMA⁺ cations, extending to or beyond the fourth molecular layer beneath the liquid surface.

Local structure of liquid/vapour interfaces approaching the critical point

Investigating the structure of fluid interfaces at high temperatures is a particularly delicate task that requires effective ways of discriminating liquid from vapour and identifying the location of the liquid phase boundary, thereby allowing to distinguish intrinsic from capillary fluctuations. Several numerical approaches require introducing a coarse-graining length scale, often heuristically chosen to be the molecular size, to determine the location of the liquid phase boundary. Here, we propose an alternative rationale for choosing this coarse-graining length scale; we require the average position of the local liquid phase dividing surface to match its flat, macroscopic counterpart. We show that this approach provides additional insight into the structure of the liquid/vapour interface, suggesting the presence of another length scale beyond the bulk correlation one that plays an important role in determining the interface structure.

Molecular Dynamics Investigation of Nanoscale Hydrophobicity of Polymer Surfaces: What Makes Water Wet?

The wettability of a polymer surface─related to its hydrophobicity or tendency to repel water─can be crucial for determining its utility, such as for a coating or a purification membrane. While wettability is commonly associated with the macroscopic measurement of a contact angle between surface, water, and air, the molecular physics that underlie these macroscopic observations are not fully known, and anticipating the relative behavior of different polymers is challenging. To address this gap in molecular-level understanding, we use molecular dynamics simulations to investigate and contrast interactions of water with six chemically distinct polymers: polytetrafluoroethylene, polyethylene, polyvinyl chloride, poly(methyl methacrylate), Nylon-66, and poly(vinyl alcohol). We show that several prospective quantitative metrics for hydrophobicity agree well with experimental contact angles. Moreover, the behavior of water in proximity to these polymer surfaces can be distinguished with analysis of interfacial water dynamics, extent of hydrogen bonding, and molecular orientation─even when macroscopic measures of hydrophobicity are similar. The predominant factor dictating wettability is found to be the extent of hydrogen bonding between polymer and water, but the precise manifestation of hydrogen bonding and its impact on surface water structure varies. In the absence of hydrogen bonding, other molecular interactions and polymer mechanics control hydrophobic ordering. These results provide new insights into how polymer chemistry specifically impacts water-polymer interactions and translates to surface hydrophobicity. Such factors may facilitate the design or processing of polymer surfaces to achieve targeted wetting behavior, and presented analyses can be useful in studying the interfacial physics of other systems.

Surface viscosity in simple liquids

The response of Newtonian liquids to small perturbations is usually considered to be fully described by homogeneous transport coefficients like shear and dilatational viscosity. However, the presence of strong density gradients at the liquid/vapor boundary of fluids hints at the possible existence of an inhomogeneous viscosity. Here, we show that a surface viscosity emerges from the collective dynamics of interfacial layers in molecular simulations of simple liquids. We estimate the surface viscosity to be 8-16 times smaller than that of the bulk fluid at the thermodynamic point considered. This result can have important implications for reactions at liquid surfaces in atmospheric chemistry and catalysis.

High-density liquid (HDL) adsorption at the supercooled water/vapor interface and its possible relation to the second surface tension inflection point

We investigate the properties of water along the liquid/vapor coexistence line in the supercooled regime down to the no-man's land. Extensive molecular dynamics simulations of the TIP4P/2005 liquid/vapor interface in the range 198-348 K allow us to locate the second surface tension inflection point with a high accuracy at 283 ± 5 K, close to the temperature of maximum density. This temperature also coincides with the appearance of a density anomaly at the interface known as the apophysis. We relate the emergence of the apophysis to the observation of high-density liquid (HDL) water adsorption in the proximity of the liquid/vapor interface.

Surface Properties of N,N-Dimethylformamide-Water Mixtures, As Seen from Computer Simulations

The liquid-vapor interface of N,N-dimethylformamide (DMF)-water mixtures, spanning the entire composition range, is investigated in detail at 298 K by molecular dynamics simulation and intrinsic surface analysis. DMF molecules are found to adsorb strongly at the liquid surface, but this adsorption extends only to the first molecular layer. Water and DMF molecules mix with each other on the molecular scale even in the surface layer; thus, no marked self-association of any of the components is seen at the liquid surface. The major surface component prefers such orientation in which the molecular dipole vector lays parallel with the macroscopic plane of the surface. On the other hand, the preferred orientation of the minor component is determined, at both ends of the composition range, by the possibility of H-bond formation with the major component. The lack of H-donating ability of DMF leads to a rapid breakup of the percolating H-bond network at the surface; due to the strong adsorption of DMF, this breakup occurs below the bulk phase DMF mole fraction of 0.03. The disruption of the surface H-bond network also accelerates the exchange of both species between the liquid surface and bulk liquid phase, although, for water, this effect becomes apparent only above a bulk phase DMF mole fraction of 0.4. H-bonds formed by a DMF and a water molecule live, on average, 25-60% longer than those formed by two water molecules at the liquid surface. A similar, but smaller (i.e., about 10-20%) difference is seen in the bulk liquid phase. The enhanced surface mobility of the molecules results in 2-6 times larger diffusion coefficient and 2-5 times shorter H-bond lifetime values at the liquid surface than in the bulk liquid phase. The diffusion of both molecules is slowed down in the presence of the other species; in the case of DMF, this effect is caused by the formation of water-DMF H-bonds, whereas for water, steric hindrances imposed by the bulky DMF neighbors are responsible for this slowing down.

Molecular Dynamics Simulations of Self-Assembling Colloids in Fed-State Human Intestinal Fluids and Their Solubilization of Lipophilic Drugs

Bioavailability of oral drugs often depends on how soluble the active pharmaceutical ingredient is in the fluid present in the small intestine. For efficient drug discovery and development, computational tools are needed for estimating this drug solubility. In this paper, we examined human intestinal fluids collected in the fed state, with coarse-grained molecular dynamics simulations. The experimentally obtained concentrations in aspirated duodenal fluids from five healthy individuals were used in three simulation sets to evaluate the importance of the initial distribution of molecules and the presence of glycerides in the simulation box when simulating the colloidal environment of the human intestinal fluid. We observed self-assembly of colloidal structures of different types: prolate, elongated, and oblate micelles, and vesicles. Glycerides were important for the formation of vesicles, and their absence was shown to induce elongated micelles. We then simulated the impact of digestion and absorption on the different colloidal types. Finally, we looked at the solubilization of three model compounds of increasing lipophilicity (prednisolone, fenofibrate, and probucol) by calculating contact ratios of drug-colloid to drug-water. Our simulation results of colloidal interactions with APIs were in line with experimental solubilization data but showed a dissimilarity to solubility values when comparing fasted-/fed-state ratios between two of the APIs. This work shows that coarse-grained molecular dynamics simulation is a promising tool for investigation of the intestinal fluids, in terms of colloidal attributes and drug solubility.

Effect of sodium chloride adsorption on the surface premelting of ice

We characterise the structural properties of the quasi-liquid layer (QLL) at two low-index ice surfaces in the presence of sodium chloride (Na⁺/Cl^-) ions by molecular dynamics simulations. We find that the presence of a high surface density of Na⁺/Cl^- pairs changes the surface melting behaviour from step-wise to gradual melting. The ions lead to an overall increase of the thickness and the disorder of the QLL, and to a low-temperature roughening transition of the air-ice interface. The local molecular structure of the QLL is similar to that of liquid water, and the differences between the basal and primary prismatic surface are attenuated by the presence of Na⁺/Cl^- pairs. These changes modify the crystal growth rates of different facets and the solvation environment at the surface of sea-water ice with a potential impact on light scattering and environmental chemical reactions.

Critical Thicknesses of Free-Standing Thin Films of Molten Polymers: A Multiscale Simulation Study

The free-standing thin films of melted poly(ethylene oxide) have been extensively simulated by the chemically specific coarse-grained (CG) molecular dynamics (MD) method. It is revealed that if the polymer thin film becomes thinner than some critical value, it would initially turn into a fiber, accompanied by an increase in the free surface area and a decrease in surface tension. A simple but efficient scheme is proposed to determine the critical interfacial thickness and the film thickness from the non-intrinsic density and pressure profiles, and the ratio of the two thicknesses is defined as the interfacial fraction. The critical film thickness is found to increase with the number of chains or equivalently the transverse area. With increasing temperature, the critical interfacial thickness increases a bit whereas the critical film thickness slightly decreases, highlighting the important role of the interfacial fraction. For both of the "critical" and "thick" films, the outermost surface layers are confirmed to undergo the greatest movements. The "critical" film exhibits the intrinsic interfacial thickness and bulk density almost identical to those of the "thick" film, dictating the thickness independence of the surface tension. Therefore, the phase stability of the film is essentially determined from the intrinsic thickness of the bulk layer, and the identified temperature dependence of the critical film thickness can be mainly explained by the surface tension.

Investigation of the Second Harmonic Generation at the Water-Vacuum Interface by Using Multi-Scale Modeling Methods

The Sequential Quantum Mechanics/Molecular Mechanics scheme has been enacted to perform a systematic investigation of the polarizability (α) and first hyperpolarizability (β) responses at the water-vacuum interface. After performing classical molecular dynamics simulations to provide snapshots of the structures, quantum chemistry calculations of the linear and nonlinear optical responses have been performed for clusters of five water molecules at the time-dependent DFT level in combination with different embedding schemes, ranging from point charges to polarizable point charges, with and without local field effects. When going from the bulk to the interface, the main observations of these calculations encompass i) a modest increase of the average polarizability but an increase by about a factor of two of its anisotropy, ii) an increase by about 20 % of the β_HRS response, accompanied by a small increase of its depolarization ratio, and iii) a net increase of the component of the β tensor normal to the interface (β_zzz ) as well as of β_// . Globally, the interfacial effects on β are localized at the first molecular layer while they are observed up to the fourth molecular layer on α.

The Role of Surface Chemistry in the Orientational Behavior of Water at an Interface

Molecular dynamics studies have demonstrated that molecular water at an interface, with either a gas or a solid, displays anisotropic orientational behavior in contrast to its bulk counterpart. This effect has been recently implicated in the like-charge attraction problem for colloidal particles in solution. Here, negatively charged particles in solution display a long-ranged attraction where continuum electrostatic theory predicts monotonically repulsive interactions, particularly in solutions with monovalent salt ions at low ionic strength. Anisotropic orientational behavior of solvent molecules at an interface gives rise to an excess interfacial electrical potential which we suggest generates an additional solvation contribution to the total free energy that is traditionally overlooked in continuum descriptions of interparticle interactions in solution. In the present investigation we perform molecular dynamics simulation based calculations of the interfacial potential using realistic surface models representing various chemistries as well as different solvents. Similar to previous work that focused on simple model surfaces constructed by using oxygen atoms, we find that solvents at more realistic model surfaces exhibit substantial anisotropic orientational behavior. We explore the dependence of the interfacial solvation potential on surface properties such as surface group chemistry and group density at silica and carboxylated polystyrene interfaces. For water, we note surprisingly good agreement between results obtained for a simple O-atom wall and more complex surface models, suggesting a general qualitative consistency of the interfacial solvation effect for surfaces in contact with water. In contrast, for an aprotic solvent such as DMSO, surface chemistry appears to exert a stronger influence on the sign and magnitude of the interfacial solvation potential. The study carries broad implications for molecular-scale interactions and may find relevance in explaining a range of phenomena in soft-matter physics and cell biology.

Computer Simulation of the Surface of Aqueous Ionic and Surfactant Solutions

The surface of aqueous solutions of simple salts was not the main focus of scientific attention for a long while. Considerable interest in studying such systems has only emerged in the past two decades, following the pioneering finding that large halide ions, such as I^-, exhibit considerable surface affinity. Since then, a number of issues have been clarified; however, there are still several unresolved points (e.g., the effect of various salts on lateral water diffusion at the surface) in this respect. Computer simulation studies of the field have largely benefited from the appearance of intrinsic surface analysis methods, by which the particles staying right at the boundary of the two phases can be unambiguously identified. Considering complex ions instead of simple ones opens a number of interesting questions, both from the theoretical point of view and from that of the applications. Besides reviewing the state-of-the-art of intrinsic surface analysis methods as well as the most important advances and open questions concerning the surface of simple ionic solutions, we focus on two such systems in this Perspective, namely, the surface of aqueous mixtures of room temperature ionic liquids and that of ionic surfactants. In the case of the former systems, for which computer simulation studies have still scarcely been reported, we summarize the theoretical advances that could trigger such investigations, which might well be of importance also from the point of view of industrial applications. Computer simulation methods are, on the other hand, widely used in studies of the surface of surfactant solutions. Here we review the most important theoretical advances and issues to be addressed and discuss two areas of applications, namely, the inclusion of information gathered from such simulations in large scale atmospheric models and the better understanding of the airborne transmission of viruses, such as SARS-CoV-2.

How to Characterize Amorphous Shapes: The Tale of a Reverse Micelle

Aerosol-OT reverse micelles represent a chemical construct where surfactant molecules self-assemble to stabilize water nanodroplets 1-10 nm in diameter. Although commonly assumed to adopt a spherical shape, all-atom molecular dynamics simulations and some experimental studies predict a nonspherical shape. If these aggregates are not spherical, then what shape do they take? Because the tools needed to evaluate the shape of something that lacks regular structure, order, or symmetry are not well developed, we present a set of three intuitive metrics─coordinate-pair eccentricity, convexity, and the curvature distribution─that estimate the shape of an amorphous object, and we demonstrate their use on a simulated aerosol-OT reverse micelle. These metrics are all well-established methods and principles in mathematics, and each provides unique information about the shape. Together, these metrics provide intuitive descriptions of amorphous shapes, facilitate ways to quantify those shapes, and follow their changes over time.

Explicit-pH Coarse-Grained Molecular Dynamics Simulations Enable Insights into Restructuring of Intestinal Colloidal Aggregates with Permeation Enhancers

Permeation enhancers (PEs) can increase the bioavailability of drugs. The mechanisms of action of these PEs are complex, but, typically, when used for oral administration, they can transiently induce the alteration of trans- and paracellular pathways, including increased solubilization and membrane fluidity, or the opening of the tight junctions. To elucidate these mechanistic details, it is important to understand the aggregation behavior of not only the PEs themselves but also other molecules already present in the intestine. Aggregation processes depend critically on, among other factors, the charge state of ionizable chemical groups, which is affected by the pH of the system. In this study, we used explicit-pH coarse-grained molecular dynamics simulations to investigate the aggregation behavior and pH dependence of two commonly used PEs—caprate and SNAC—together with other components of fasted- and fed-state simulated intestinal fluids. We also present and validate a coarse-grained molecular topology for the bile salt taurocholate suitable for the Martini3 force-field. Our results indicate an increase in the number of free molecules as a function of the system pH and for each combination of FaSSIF/FeSSIF and PEs. In addition, there are differences between caprate and SNAC, which are rationalized based on their different molecular structures and critical micelle concentrations.

Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies

As molecular dynamics simulations increase in complexity, new analysis tools are necessary to facilitate interpreting the results. Lipids, for instance, are known to form many complicated morphologies, because of their amphipathic nature, becoming more intricate as the particle count increases. A few lipids might form a micelle, where aggregation of tens of thousands could lead to vesicle formation. Millions of lipids comprise a cell and its organelle membranes, and are involved in processes such as neurotransmission and transfection. To study such phenomena, it is useful to have analysis tools that understand what is meant by emerging entities such as micelles and vesicles. Studying such systems at the particle level only becomes extremely tedious, counterintuitive, and computationally expensive. To address this issue, we developed a method to track all the individual lipid leaflets, allowing for easy and quick detection of topological changes at the mesoscale. By using a voxel-based approach and focusing on locality, we forego costly geometrical operations without losing important details and chronologically identify the lipid segments using the Jaccard index. Thus, we achieve a consistent sequential segmentation on a wide variety of (lipid) systems, including monolayers, bilayers, vesicles, inverted hexagonal phases, up to the membranes of a full mitochondrion. It also discriminates between adhesion and fusion of leaflets. We show that our method produces consistent results without the need for prefitting parameters, and segmentation of millions of particles can be achieved on a desktop machine.

Energy-Based Interface Detection for Phase Change Processes of Monatomic Fluids in Nanoconfinements

An energy-based liquid-vapor interface detection method is presented using molecular dynamics simulations of liquid menisci confined between two parallel plates under equilibrium and evaporation/condensation conditions. This method defines the liquid-vapor interface at the location where the average kinetic energy of atoms first exceeds the average potential energy imposed by all neighboring molecules. This definition naturally adapts to the location of the menisci relative to the walls and can properly model the behavior of the liquid adsorbed layers. Unlike the density cutoff methods frequently used in the literature that suffer from density layering effects, this new method gives smooth and continuous liquid-vapor interfaces in nanoconfinements. Surface tension values calculated from the equilibrium MD simulations match the Young-Laplace equation better when using the radius of curvatures calculated from this method. Overall, this energy-based liquid-vapor interface detection method can be used in studies of nanoscale phase change processes and other relevant applications.

Monolayer Structures of Supramolecular Antagonistic Salt Aggregates

The speculated presence of monomolecular lamellae of antagonistic salts in oil-water mixtures has left several open questions besides their hypothetical existence, including their microscopic structure and stabilization mechanism. Here, we simulate the spontaneous formation of supramolecular aggregates of the antagonistic salt sodium tetraphenylborate (NaBPh₄) in water and 3-methylpyridine (3-MP) at the atomistic level. We show that, indeed, the lamellae are formed by a monomolecular layer of the anion, enveloped by 3-MP and hydrated sodium counterions. To understand which thermodynamic forces drive the aggregation, we compare the full-atomistic model with a simplified one for the salt and show that the strong hydrophobic effect granted by the large excluded volume of the anion, together with electrostatic repulsion, suffice to explain the stability of the monomolecular lamellae.

Hydrogen bond dynamics of interfacial water molecules revealed from two-dimensional vibrational sum-frequency generation spectroscopy

Vibrational sum-frequency generation (vSFG) spectroscopy allows the study of the structure and dynamics of interfacial systems. In the present work, we provide a simple recipe, based on a narrowband IR pump and broadband vSFG probe technique, to computationally obtain the two-dimensional vSFG spectrum of water molecules at the air-water interface. Using this technique, to study the time-dependent spectral evolution of hydrogen-bonded and free water molecules, we demonstrate that at the interface, the vibrational spectral dynamics of the free OH bond is faster than that of the bonded OH mode.

Single-Particle Dynamics at the Intrinsic Surface of Aqueous Alkali Halide Solutions

The distribution of ions in the proximity of the liquid-vapor interface of their aqueous solution has been the subject of an intense debate during the last decade. The effects of ionic polarizability have been one of its salient aspects. Much less has been said about the corresponding dynamical properties, which are substantially unexplored. Here, we investigate the single-particle dynamics at the liquid-vapor interface of several alkali halide solutions, using molecular dynamics simulations with polarizable and nonpolarizable force fields and intrinsic surface analysis. We analyze the diffusion coefficient, residence time, and velocity autocorrelation function of water and ions and investigate how these properties depend on the molecular layer where they reside. While anions are found in the first molecular layer for relatively long times, cations are only making quick excursions into it, thanks to thermal fluctuations. The in-layer residence time of ions and their molar fraction in the layer turned out to be linearly dependent on each other. We interpret this unexpected result using a simple two-state model. In addition, we found that, unlike water and other neat molecular liquids that show a different diffusion mechanism at the surface than in the bulk of their liquid phase, ions do not enjoy enhanced mobility in the surface layer of their aqueous solution. This result indicates that ions in the surface layer are shielded by their nearest water neighbors from being exposed to the vapor phase as much as possible. Such positions are available for the ions at the negatively curved troughs of the molecularly rugged liquid surface.

An embedded atom model for Ga-Pd systems: From intermetallic crystals to liquid alloys

We present an embedded atom model (EAM) potential for modeling Ga-Pd interactions within intermetallic solids and liquid alloys. The molecular mechanics potential was parameterized on the basis of the structure and mechanical properties of GaPd₂, whereas a series of other Ga_xPd_1-x phases and liquid alloy systems allowed rigorous benchmarking. For the intermetallic solids, structures and elastic moduli were found in very reasonable agreement with experimental structures and results from DFT calculations. The liquid models were characterized from molecular dynamics simulations that also showed nice agreement with experimental and ab initio reference data. Moreover, the perspectives of the EAM model are illustrated by the elucidation of an alloy nanodroplet model whose characterization includes the kinetics of Pd dopant diffusion from the Ga droplet surface to the bulk liquid and vice versa.

An octanol hinge opens the door to water transport

Despite their prevalent use as a surrogate for partitioning of pharmacologically active solutes across lipid membranes, the mechanism of transport across water/octanol phase boundaries has remained unexplored. Using molecular dynamics, graph theoretical, cluster analysis, and Langevin dynamics, we reveal an elegant mechanism for the simplest solute, water. Self-assembled octanol at the interface reversibly binds water and swings like the hinge of a door to bring water into a semi-organized second interfacial layer (a “bilayer island”). This mechanism is distinct from well-known lipid flipping and water transport processes in protein-free membranes, highlighting important limitations in the water/octanol proxy. Interestingly, the collective and reversible behavior is well-described by a double well potential energy function, with the two stable states being the water bound to the hinge on either side of the interface. The function of the hinge for transport, coupled with the underlying double well energy landscape, is akin to a molecular switch or shuttle that functions under equilibrium and is driven by the differential free energies of solvation of H₂O across the interface. This example successfully operates within the dynamic motion of instantaneous surface fluctuations, a feature that expands upon traditional approaches toward controlled solute transport that act to avoid or circumvent the dynamic nature of the interface.

Despite their pharmacological relevance, the mechanism of transport across water/octanol phase boundaries has remained unexplored. Octanol molecular assemblies are demonstrated to reversibly bind water and swing like the hinge of a door.

Weak scaling of the contact distance between two fluctuating interfaces with system size

A pair of flat parallel surfaces, each freely diffusing along the direction of their separation, will eventually come into contact. If the shapes of these surfaces also fluctuate, then contact will occur when their centers-of-mass remain separated by a nonzero distance ℓ. An example of such a situation is the motion of interfaces between two phases at conditions of thermodynamic coexistence, and in particular the annihilation of domain wall pairs under periodic boundary conditions. Here we present a general approach to calculate the probability distribution of the contact distance ℓ and determine how its most likely value ℓ^{*} depends on the surfaces' lateral size L. Using the Edward-Wilkinson equation as a model for interfaces, we demonstrate that ℓ^{*} scales weakly with system size, i.e., the dependence of ℓ^{*} on L for both (1+1)- and (2+1)-dimensional interfaces is such that lim_{L→∞}(ℓ^{*}/L)=0. In particular, for (2+1)-dimensional interfaces ℓ^{*} is an algebraic function of logL, a result that is confirmed by computer simulations of slab-shaped domains formed under periodic boundary conditions. This weak scaling implies that such domains remain topologically intact until ℓ becomes very small compared to the lateral size of the interface, contradicting expectations from equilibrium thermodynamics.

Surface Affinity of Alkali and Halide Ions in Their Aqueous Solution: Insight from Intrinsic Density Analysis

The surface tension of all aqueous alkali halide solutions is higher than that of pure water. According to the Gibbs adsorption equation, this indicates a net depletion of these ions in the interfacial region. However, simulations and experiments show that large, soft ions, such as I^-, can accumulate at the liquid/vapor interface. The presence of a loose hydration shell is usually considered to be the reason for this behavior. In this work, we perform computer simulations to characterize the liquid-vapor interface of aqueous alkali chloride and sodium halide solutions systematically, considering all ions from Li⁺ to Cs⁺ and from F^- to I^-. Using computational methods for the removal of surface fluctuations, we analyze the structure of the interface at a dramatically enhanced resolution, showing that the positive excess originates in the very first molecular layer and that the next 3-4 layers account for the net negative excess. With the help of a fictitious system with charge-inverted ion pairs, we also show that it is not possible to rationalize the surface affinity of ions in solutions in terms of the properties of anions and cations separately. Moreover, the surface excess is generally dominated by the smaller of the two ions.

Learning Coarse-Grained Potentials for Binary Fluids

For a multiple-fluid system, CG models capable of accurately predicting the interfacial properties as a function of curvature are still lacking. In this work, we propose a new probabilistic machine learning (ML) model for learning CG potentials for binary fluids. The water-hexane mixture is selected as a typical immiscible binary liquid-liquid system. We develop a new CG force field (FF) using the Shinoda-DeVane-Klein (SDK) FF framework and compute parameters in this CG FF using the proposed probabilistic ML method. It is shown that a standard response-surface approach does not provide a unique set of parameters, as it results in a loss function with multiple shallow minima. To address this challenge, we develop a probabilistic ML approach where we compute the probability density function (PDF) of parameters that minimize the loss function. The PDF has a well-defined peak corresponding to a unique set of parameters in the CG FF that reproduces the desired properties of a liquid-liquid interface. We compare the performance of the new CG FF with several existing FFs for the water-hexane mixture, including two atomistic and three CG FFs with respect to modeling the interface structure and thermodynamic properties. It is demonstrated that the new FF significantly improves the CG model prediction of both the interfacial tension and structure for the water-hexane mixture.

Molecular Mechanism of Gas Solubility in Liquid: Constant Chemical Potential Molecular Dynamics Simulations

Accurate prediction of gas solubility in a liquid is crucial in many areas of chemistry, and a detailed understanding of the molecular mechanism of the gas solvation continues to be an active area of research. Here, we extend the idea of the constant chemical potential molecular dynamics (CμMD) approach to the calculation of the gas solubility in the liquid under constant gas chemical potential conditions. As a representative example, we utilize this method to calculate the isothermal solubility of carbon dioxide in water. Additionally, we provide microscopic insight into the mechanism of solvation that preferentially occurs in areas of the surface where the hydrogen network is broken.

Time-dependent vibrational sum-frequency generation spectroscopy of the air-water interface

Vibrational sum-frequency generation spectroscopy is a powerful method to study the microscopic structure and dynamics of interfacial systems. Here we demonstrate a simple computational approach to calculate the time-dependent, frequency-resolved vibrational sum-frequency generation spectrum (TD-vSFG) of the air-water interface. Using this approach, we show that at the air-water interface, the transition of water molecules with bonded OH modes to free OH modes occurs at a time scale of $$\sim$$ ~ 3 ps, whereas water molecules with free OH modes rapidly make a transition to a hydrogen-bonded state within $$\sim$$ ~ 2 ps. Furthermore, we also elucidate the origin of the observed differential dynamics based on the time-dependent evolution of water molecules in the different local solvent environments.

Pytim: A python package for the interfacial analysis of molecular simulations

Pytim is a versatile python framework for the analysis of interfacial properties in molecular simulations. The code implements several algorithms for the identification of instantaneous interfaces of arbitrary shape, and analysis tools written specifically for the study of interfacial properties, such as intrinsic profiles. The code is written in the python language, and makes use of the numpy and scipy packages to deliver high computational performances. Pytim relies on the MDAnalysis library to analyze the trajectory file formats of popular simulation packages such as gromacs, charmm, namd, lammps or Amber, and can be used to steer OpenMM simulations. Pytim can write information about surfaces and surface atomic layers to vtk, cube, and pdb files for easy visualization. The classes of Pytim can be easily customized and extended to include new interfacial algorithms or analysis tools. The code is available as open source and is free of charge. © 2018 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.