Size-Pore-Dependent Methanol Sequestration from Water-Methanol Mixtures by an Embedded Graphene Slit.

The separation of liquid mixture components is relevant to many applications-ranging from water purification to biofuel production-and is a growing concern related to the UN Sustainable Development Goals (SDGs), such as "Clean water and Sanitation" and "Affordable and clean energy". One promising technique is using graphene slit-pores as filters, or sponges, because the confinement potentially affects the properties of the mixture components in different ways, favoring their separation. However, no systematic study has shown how the size of a pore changes the thermodynamics of the surrounding mixture. Here, we focus on water-methanol mixtures and explore, using Molecular Dynamics simulations, the effects of a graphene pore, with size ranging from 6.5 to 13 Å, for three compositions: pure water, 90%-10%, and 75%-25% water-methanol. We show that tuning the pore size can change the mixture pressure, density and composition in bulk due to the size-dependent methanol sequestration within the pore. Our results can help in optimizing the graphene pore size for filtering applications.

Structure and dynamics of nanoconfined water and aqueous solutions.

This review is devoted to discussing recent progress on the structure, thermodynamic, reactivity, and dynamics of water and aqueous systems confined within different types of nanopores, synthetic and biological. Currently, this is a branch of water science that has attracted enormous attention of researchers from different fields interested to extend the understanding of the anomalous properties of bulk water to the nanoscopic domain. From a fundamental perspective, the interactions of water and solutes with a confining surface dramatically modify the liquid's structure and, consequently, both its thermodynamical and dynamical behaviors, breaking the validity of the classical thermodynamic and phenomenological description of the transport properties of aqueous systems. Additionally, man-made nanopores and porous materials have emerged as promising solutions to challenging problems such as water purification, biosensing, nanofluidic logic and gating, and energy storage and conversion, while aquaporin, ion channels, and nuclear pore complex nanopores regulate many biological functions such as the conduction of water, the generation of action potentials, and the storage of genetic material. In this work, the more recent experimental and molecular simulations advances in this exciting and rapidly evolving field will be reported and critically discussed.

Advances in the study of supercooled water.

In this review, we report recent progress in the field of supercooled water. Due to its uniqueness, water presents numerous anomalies with respect to most simple liquids, showing polyamorphism both in the liquid and in the glassy state. We first describe the thermodynamic scenarios hypothesized for the supercooled region and in particular among them the liquid-liquid critical point scenario that has so far received more experimental evidence. We then review the most recent structural indicators, the two-state model picture of water, and the importance of cooperative effects related to the fact that water is a hydrogen-bonded network liquid. We show throughout the review that water's peculiar properties come into play also when water is in solution, confined, and close to biological molecules. Concerning dynamics, upon mild supercooling water behaves as a fragile glass former following the mode coupling theory, and it turns into a strong glass former upon further cooling. Connections between the slow dynamics and the thermodynamics are discussed. The translational relaxation times of density fluctuations show in fact the fragile-to-strong crossover connected to the thermodynamics arising from the existence of two liquids. When considering also rotations, additional crossovers come to play. Mobility-viscosity decoupling is also discussed in supercooled water and aqueous solutions. Finally, the polyamorphism of glassy water is considered through experimental and simulation results both in bulk and in salty aqueous solutions. Grains and grain boundaries are also discussed.

In Silico Evidence That Protein Unfolding is a Precursor of Protein Aggregation.

We present a computational study on the folding and aggregation of proteins in an aqueous environment, as a function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding of the native conformation without the occurrence of aggregates. A further increment of the protein concentration results in the complete loss of the folded structures and induces the formation of protein aggregates. We discuss the effect of the protein interface on the water fluctuations in the protein hydration shell and their relevance in the protein-protein interaction.

Contribution of Water to Pressure and Cold Denaturation of Proteins.

The mechanisms of cold and pressure denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here, we study several cases of proteins, with or without a unique native state, with or without hydrophilic residues, by means of a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that taking into account how water at the protein interface changes its hydrogen bond properties and its density fluctuations is enough to predict protein stability regions with elliptic shapes in the temperature-pressure plane, consistent with previous theories. Our results clearly identify the different mechanisms with which water participates to denaturation and open the perspective to develop advanced computational design tools for protein engineering.

Structural behavior and dynamics of an anomalous fluid between attractive and repulsive walls: templating, molding, and superdiffusion.

Confinement can modify the dynamics, the thermodynamics, and the structural properties of liquid water, the prototypical anomalous liquid. By considering a generic model for anomalous liquids, suitable for describing solutions of globular proteins, colloids, or liquid metals, we study by molecular dynamics simulations the effect that an attractive wall with structure and a repulsive wall without structure have on the phases, the crystal nucleation, and the dynamics of the fluid. We find that at low temperatures the large density of the attractive wall induces a high-density, high-energy structure in the first layer ("templating" effect). In turn, the first layer induces a "molding" effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range influence thanks to a sequence of templating, molding, and templating effects through the layers. We find that the walls also have an influence on the dynamics of the liquid, with a stronger effect near the attractive wall. In particular, we observe that the dynamics is largely heterogeneous (i) among the layers, as a consequence of the sequence of structures caused by the walls presence, and (ii) within the same layer, due to superdiffusive liquid veins within a frozen matrix of particles near the walls at low temperature and high density. Hence, the partial freezing of the first layer does not correspond necessarily to an effective reduction of the channel's section in terms of transport properties, as suggested by other authors.

More than one dynamic crossover in protein hydration water.

Studies of liquid water in its supercooled region have helped us better understand the structure and behavior of water. Bulk water freezes at its homogeneous nucleation temperature (approximately 235 K), but protein hydration water avoids this crystallization because each water molecule binds to a protein. Here, we study the dynamics of the hydrogen bond (HB) network of a percolating layer of water molecules and compare the measurements of a hydrated globular protein with the results of a coarse-grained model that successfully reproduces the properties of hydration water. Using dielectric spectroscopy, we measure the temperature dependence of the relaxation time of proton charge fluctuations. These fluctuations are associated with the dynamics of the HB network of water molecules adsorbed on the protein surface. Using Monte Carlo simulations and mean-field calculations, we study the dynamics and thermodynamics of the model. Both experimental and model analyses are consistent with the interesting possibility of two dynamic crossovers, (i) at approximately 252 K and (ii) at approximately 181 K. Because the experiments agree with the model, we can relate the two crossovers to the presence at ambient pressure of two specific heat maxima. The first is caused by fluctuations in the HB formation, and the second, at a lower temperature, is due to the cooperative reordering of the HB network.

Small-angle X-ray scattering unveils the internal structure of lipid nanoparticles.

Lipid nanoparticles own a remarkable potential in nanomedicine, only partially disclosed. While the clinical use of liposomes and cationic lipid-nucleic acid complexes is well-established, liquid lipid nanoparticles (nanoemulsions), solid lipid nanoparticles, and nanostructured lipid carriers have even greater possibilities. However, they face obstacles in being used in clinics due to a lack of understanding about the molecular mechanisms controlling their drug loading and release, interactions with the biological environment (such as the protein corona), and shelf-life stability. To create effective drug delivery carriers and successfully translate bench research to clinical settings, it is crucial to have a thorough understanding of the internal structure of lipid nanoparticles. Through synchrotron small-angle X-ray scattering experiments, we determined the spatial distribution and internal structure of the nanoparticles' lipid, surfactant, and the bound water in them. The nanoparticles themselves have a barrel-like shape that consists of coplanar lipid platelets (specifically cetyl palmitate) that are covered by loosely spaced polysorbate 80 surfactant molecules, whose polar heads retain a large amount of bound water. To reduce the interface cost of bound water with unbound water without stacking, the platelets collapse onto each other. This internal structure challenges the classical core-shell model typically used to describe solid lipid nanoparticles and could play a significant role in drug loading and release, biological fluid interaction, and nanoparticle stability, making our findings valuable for the rational design of lipid-based nanoparticles.

Effect of hydrogen bond cooperativity on the behavior of water.

Four scenarios have been proposed for the low-temperature phase behavior of liquid water, each predicting different thermodynamics. The physical mechanism that leads to each is debated. Moreover, it is still unclear which of the scenarios best describes water, because there is no definitive experimental test. Here we address both open issues within the framework of a microscopic cell model by performing a study combining mean-field calculations and Monte Carlo simulations. We show that a common physical mechanism underlies each of the four scenarios, and that two key physical quantities determine which of the four scenarios describes water: (i) the strength of the directional component of the hydrogen bond and (ii) the strength of the cooperative component of the hydrogen bond. The four scenarios may be mapped in the space of these two quantities. We argue that our conclusions are model independent. Using estimates from experimental data for H-bond properties the model predicts that the low-temperature phase diagram of water exhibits a liquid-liquid critical point at positive pressure.

Correction: March et al. Protein Unfolding and Aggregation near a Hydrophobic Interface. Polymers 2021, 13, 156.

In the original publication [...].

Many-Body Contributions in Water Nanoclusters.

Many-body interactions in water are known to be important but difficult to treat in atomistic models and often are included only as a correction. Polarizable models treat them explicitly, with long-range many-body potentials, within their classical approximation. However, their calculation is computationally expensive. Here, we evaluate how relevant the contributions to the many-body interaction associated with different coordination shells are. We calculate the global energy minimum, and the corresponding configuration, for nanoclusters of up to 20 water molecules. We find that including the first coordination shell, i.e., the five-body term of the central molecule, is enough to approximate within 5% the global energy minimum and its structure. We show that this result is valid for three different polarizable models, the Dang-Chang, the MB-pol, and the Kozack-Jordan potentials. This result suggests a strategy to develop many-body potentials for water that are reliable and, at the same time, computationally efficient.

Hydrophobic Homopolymer's Coil-Globule Transition and Adsorption onto a Hydrophobic Surface under Different Conditions.

Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we use Monte Carlo calculations of a coarse-grained model incorporating water's effects on the system's free energy. Following previous studies, we modeled an unstructured protein as a polymer chain. Because we are interested in investigating how it responds to thermodynamic changes near a hydrophobic surface under different conditions, we chose an entirely hydrophobic sequence to maximize the interaction with the interface. We show that a slit pore confinement without top-down symmetry enhances the unfolding and adsorption of the chain in both random coil and globular states. Moreover, we demonstrate that the hydration water modulates this behavior depending on the thermodynamic parameters. Our findings provide insights into how homopolymers and possibly unstructured proteins can sense and adjust to external stimuli such as nanointerfaces or stresses.

Homogeneous crystal nucleation near a metastable fluid-fluid phase transition.

Several scenarios exist for the protein crystallization and aggregation in solutions near a metastable fluid-fluid phase separation below the solubility line. Based on computations, it was proposed that the fluid-fluid critical point enhances the crystallization rate by many orders of magnitude, while, based on experiments, it was proposed that the fluid-fluid spinodal controls the crystallization rate. Using molecular dynamic simulations for an isotropic model with sticky interaction, we show that neither of these scenarios adequately describes the crystallization mechanism near a metastable fluid-fluid phase separation. We find that the emergence of the high-density fluid inside the spinodal drastically enhances the crystal nucleation in the subcritical region following Ostwald's rule of stages.

Confinement of anomalous liquids in nanoporous matrices.

Using molecular dynamics simulations, we investigate the effects of different nanoconfinements on complex liquids-e.g., colloids or protein solutions-with density anomalies and a liquid-liquid phase transition (LLPT). In all the confinements, we find a strong depletion effect with a large increase in liquid density near the confining surface. If the nanoconfinement is modeled by an ordered matrix of nanoparticles, we find that the anomalies are preserved. On the contrary, if the confinement is modeled by a disordered matrix of nanoparticles, we find a drastically different phase diagram: the LLPT shifts to lower pressures and temperatures, and the anomalies become weaker, as the disorder increases. We find that the density heterogeneities induced by the disordered matrix are responsible for the weakening of the LLPT and the disappearance of the anomalies.

Effect of pressure on the anomalous response functions of a confined water monolayer at low temperature.

We study a coarse-grained model for a water monolayer that cannot crystallize due to the presence of confining interfaces, such as protein powders or inorganic surfaces. Using both Monte Carlo simulations and mean field calculations, we calculate three response functions: the isobaric specific heat C(P), the isothermal compressibility K(T), and the isobaric thermal expansivity α(P). At low temperature T, we find two distinct maxima in C(P), K(T), and ∣α(P)∣, all converging toward a liquid-liquid critical point (LLCP) with increasing pressure P. We show that the maximum in C(P) at higher T is due to the fluctuations of hydrogen (H) bond formation and that the second maximum at lower T is due to the cooperativity among the H bonds. We discuss a similar effect in K(T) and ∣α(P)∣. If this cooperativity were not taken into account, both the lower-T maximum and the LLCP would disappear. However, comparison with recent experiments on water hydrating protein powders provides evidence for the existence of the lower-T maximum, supporting the hypothesized LLCP at positive P and finite T. The model also predicts that when P moves closer to the critical P the C(P) maxima move closer in T until they merge at the LLCP. Considering that other scenarios for water are thermodynamically possible, we discuss how an experimental measurement of the changing separation in T between the two maxima of C(P) as P increases could determine the best scenario for describing water.

Large decrease of fluctuations for supercooled water in hydrophobic nanoconfinement.

Using Monte Carlo simulations, we study a coarse-grained model of a water layer confined in a fixed disordered matrix of hydrophobic nanoparticles at different particle concentrations c. For c=0, we find a first-order liquid-liquid phase transition (LLPT) ending in one critical point at low pressure P. For c>0, our simulations are consistent with a LLPT line ending in two critical points at low and high P. For c=25%, at high P and low temperature, we find a dramatic decrease of compressibility, thermal expansion coefficient, and specific heat. Surprisingly, the effect is present also for c as low as 2.4%. We conclude that even a small presence of hydrophobic nanoparticles can drastically suppress thermodynamic fluctuations, making the detection of the LLPT more difficult.

Protein Unfolding and Aggregation near a Hydrophobic Interface.

The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we study how the presence of a hydrophobic surface affects this course of events. To this goal, we use a coarse-grained model of proteins and study by simulations their folding and aggregation near an ideal hydrophobic surface in an aqueous environment by changing parameters such as temperature and hydrophobic strength, related, e.g., to ions concentration. We show that the hydrophobic surface, as well as the other parameters, affect both the protein unfolding and aggregation. We discuss the interpretation of these results and define future lines for further analysis, with their possible implications in neurodegenerative diseases.

Nanoconfined Fluids: Uniqueness of Water Compared to Other Liquids.

Nanoconfinement can drastically change the behavior of liquids, puzzling us with counterintuitive properties. It is relevant in applications, including decontamination and crystallization control. However, it still lacks a systematic analysis for fluids with different bulk properties. Here we address this gap. We compare, by molecular dynamics simulations, three different liquids in a graphene slit pore: (1) A simple fluid, such as argon, described by a Lennard-Jones potential; (2) an anomalous fluid, such as a liquid metal, modeled with an isotropic core-softened potential; and (3) water, the prototypical anomalous liquid, with directional HBs. We study how the slit-pore width affects the structure, thermodynamics, and dynamics of the fluids. All the fluids show similar oscillating properties by changing the pore size. However, their free-energy minima are quite different in nature: (i) are energy-driven for the simple liquid; (ii) are entropy-driven for the isotropic core-softened potential; and (iii) have a changing nature for water. Indeed, for water, the monolayer minimum is entropy driven, at variance with the simple liquid, while the bilayer minimum is energy driven, at variance with the other anomalous liquid. Also, water has a large increase in diffusion for subnm slit pores, becoming faster than bulk. Instead, the other two fluids have diffusion oscillations much smaller than water, slowing down for decreasing slit-pore width. Our results, clarifying that water confined at the subnm scale behaves differently from other (simple or anomalous) fluids under similar confinement, are possibly relevant in nanopores applications, for example, in water purification from contaminants.

Redefining the concept of hydration water near soft interfaces.

Water determines the properties of biological systems. Therefore, understanding the nature of the mutual interaction between water and biosystems is of primary importance for a proper assessment of any biological activity, e.g., the efficacy of new drugs or vaccines. A convenient way to characterize the interactions between biosystems and water is to analyze their impact on water density and dynamics in the proximity of the interfaces. It is commonly accepted that water bulk density and dynamical properties are recovered at distances of the order of 1 nm away from the surface of biological systems. This notion leads to the definition of hydration or biological water as the nanoscopic layer of water covering the surface of biosystems and to the expectation that all the effects of the water-interface interaction are limited to this thin region. Here, we review some of our latest contributions, showing that phospholipid membranes affect the water dynamics, structural properties, and hydrogen bond network at a distance that is more than twice as large as the commonly evoked ∼1nm thick layer and of the order of 2.4 nm. Furthermore, we unveil that at a shorter distance ∼0.5nm from the membrane, instead, there is an additional interface between lipid-bound and unbound water. Bound water has a structural role in the stability of the membrane. Our results imply that the concept of hydration water should be revised or extended and pave the way to a deeper understanding of the mutual interactions between water and biological systems.

Softness dependence of the anomalies for the continuous shouldered well potential.

By molecular dynamic simulations we study a system of particles interacting through a continuous isotropic pairwise core-softened potential consisting of a repulsive shoulder and an attractive well. The model displays a phase diagram with three fluid phases: a gas-liquid critical point, a liquid-liquid critical point, and anomalies in density, diffusion, and structure. The hierarchy of the anomalies is the same as for water. Here we study in a systematic way the effect on the anomalies of varying the softness of the potential. We find that, making the soft-core steeper and more penetrable, the regions of density and diffusion anomalies contract in the T-rho plane, while the region of structural anomaly is weakly affected. Therefore, a liquid can have anomalous structural behavior without having density or diffusion anomalies. We show that, by considering as effective distances those corresponding to the maxima of the first two peaks of the radial distribution function g(r) in the high-density liquid, we can generalize to continuous two-scale potentials a criterion for the occurrence of the anomalies of density and diffusion, originally proposed for discontinuous potentials. However, we observe that the knowledge of the structural behavior within the first two coordination shells of the liquid is not enough to establish, in general, the occurrence of the anomalies. By introducing the density derivative of the cumulative order integral of the excess entropy, measuring shell by shell the amount of order in the liquid, we show that the anomalous behavior is regulated by the structural order at distances as large as the fourth coordination shell. By comparing the results for different softness of the potential, we conclude that the disappearance of the density and diffusion anomalies for the steeper potentials is due to a more structured short-range order. All these results increase our understanding on how, knowing the interaction potential, we can evaluate the possible presence of anomalies for a liquid.