Structural and dynamical aspects of water in contact with a hydrophobic surface

Beyond Local Structures in Critical Supercooled Water through Unsupervised Learning

The presence of a second critical point in water has been a topic of intense investigation for the last few decades. The molecular origins underlying this phenomenon are typically rationalized in terms of the competition between local high-density (HD) and low-density (LD) structures. Their identification often requires designing parameters that are subject to human intervention. Herein, we use unsupervised learning to discover structures in atomistic simulations of water close to the liquid-liquid critical point (LLCP). Encoding the information on the environment using local descriptors, we do not find evidence for two distinct thermodynamic structures. In contrast, when we deploy nonlocal descriptors that probe instead heterogeneities on the nanometer length scale, this leads to the emergence of LD and HD domains rationalizing the microscopic origins of the density fluctuations close to criticality.

Do Machine-Learning Atomic Descriptors and Order Parameters Tell the Same Story? The Case of Liquid Water

Machine-learning (ML) has become a key workhorse in molecular simulations. Building an ML model in this context involves encoding the information on chemical environments using local atomic descriptors. In this work, we focus on the Smooth Overlap of Atomic Positions (SOAP) and their application in studying the properties of liquid water both in the bulk and at the hydrophobic air-water interface. By using a statistical test aimed at assessing the relative information content of different distance measures defined on the same data space, we investigate if these descriptors provide the same information as some of the common order parameters that are used to characterize local water structure such as hydrogen bonding, density, or tetrahedrality to name a few. Our analysis suggests that the ML description and the standard order parameters of the local water structure are not equivalent. In particular, a combination of these order parameters probing local water environments can predict SOAP similarity only approximately, and vice versa, the environments that are similar according to SOAP are not necessarily similar according to the standard order parameters. We also elucidate the role of some of the metaparameters in the SOAP definition in encoding chemical information.

Isotope effects on the structural transformation and relaxation of deeply supercooled water

We have examined the structure of supercooled liquid D2O as a function of temperature between 185 and 255 K using pulsed laser heating to rapidly heat and cool the sample on a nanosecond timescale. The liquid structure can be represented as a linear combination of two structural motifs, with a transition between them described by a logistic function centered at 218 K with a width of 10 K. The relaxation to a metastable state, which occurred prior to crystallization, exhibited nonexponential kinetics with a rate that was dependent on the initial structural configuration. When the temperature is scaled by the temperature of maximum density, which is an isostructural point of the isotopologues, the structural transition and the non-equilibrium relaxation kinetics of D2O agree remarkably well with those for H2O.

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.

Structure and dynamics of water confined in cylindrical nanopores with varying hydrophobicity

We report a detailed study of the main structural and dynamical features of water confined in model Lennard-Jones nanopores with tunable hydrophobicity and finite length ([Formula: see text] Å). The generic model of cylindrical confinement used is able to reproduce the wetting features of a large class of technologically and biologically relevant systems spanning from crystalline nanoporous materials, to mesoporous silica and ion channels. The aim of this work is to discuss the influence of parameters such as wall hydrophobicity, temperature, and pore size on the structural and dynamical features of confined water. Our simulation campaign confirmed the existence of a core domain in which water displays bulk-like structural features even in extreme ([Formula: see text] Å) confinement, while dynamical properties were shown to depend non-trivially on the size and hydrophobicity of the pores. This article is part of the theme issue 'Progress in mesoscale methods for fluid dynamics simulation'.

Structural aspects of an energy-based water classification index and the structure-dynamics link in glassy relaxation

An energy-based structural indicator for water, [Formula: see text], has been recently introduced by our group. In turn, in this work we aim at: (1) demonstrating that [Formula: see text] is indeed able to correctly classify water molecules between locally structured tetrahedral (T) and locally distorted (D) ones, circumventing the usual problem of certain previous indicators of overestimating the distorted state; (2) correlating [Formula: see text] with dynamic propensity, a measure of the molecular mobility tendency, in order to seek for the existence of a connection between structure and dynamics within the supercooled regime. More specifically, in the first part of this work we will show that [Formula: see text] accurately discriminates between merely thermally deformed local molecular arrangements and truly distorted molecules (defects). This fact will be made evident not only from radial distribution function results but also from the dynamic propensity distributions of the different kinds of molecules. In turn, we shall devote the second part of this work to finding correlations between T and D molecules with low- and high-dynamic-propensity molecules, respectively, thus revealing the existence of a link between local structure and dynamics, while also making evident the dominant role of the D molecules (defects) in the structural relaxation. Moreover, the availability of a proper molecular classification technique will enable us to study the timescale of such influence of structure on dynamics by defining a modified dynamic propensity measure and by applying it to the structured and unstructured water molecular states.

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature

A number of studies have constructed coarse-grained (CG) models of water to understand its anomalous properties. Most of these properties emerge at low temperatures, and an accurate CG model needs to be applicable to these low-temperature ranges. However, direct use of CG models parameterized from other temperatures, e.g., room temperature, encounters a problem known as transferability, as the CG potential essentially follows the form of the many-body CG free energy function. Therefore, temperature-dependent changes to CG interactions must be accounted for. The collective behavior of water at low temperature is generally a many-body process, which often motivates the use of expensive many-body terms in the CG interactions. To surmount the aforementioned problems, we apply the Bottom-Up Many-Body Projected Water (BUMPer) CG model constructed from Paper I to study the low-temperature behavior of water. We report for the first time that the embedded three-body interaction enables BUMPer, despite its pairwise form, to capture the growth of ice at the ice/water interface with corroborating many-body correlations during the crystal growth. Furthermore, we propose temperature transferable BUMPer models that are indirectly constructed from the free energy decomposition scheme. Changes in CG interactions and corresponding structures are faithfully recapitulated by this framework. We further extend BUMPer to examine its ability to predict the structure, density, and diffusion anomalies by employing an alternative analysis based on structural correlations and pairwise potential forms to predict such anomalies. The presented analysis highlights the existence of these anomalies in the low-temperature regime and overcomes potential transferability problems.

Effect of cholesterol on the hydration properties of ester and ether lipid membrane interphases

Fluorescence spectroscopy and Molecular Dynamics results show that cholesterol reduces water along the chains in ether lipids by changing the water distribution pattern between tightly and loosely bound water molecules. Water distribution was followed by emission spectra and generalized polarization of 6-dodecanoyl-2-dimethyl aminonaphthalene (Laurdan) inserted in 1,2-dimiristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine (14: 0 Diether PC) membranes. Molecular Dynamics simulations indicate that the action of cholesterol could be different in ether PC in comparison to ester PC. In addition, Cholesterol seems to act "per se" as an additional hydration center in ether lipids. Regardless of the phase state, cholesterol both in DMPC and 14:0 Diether PC vesicles, changed the distribution of water molecules decreasing the dipole relaxation of the lipid interphase generating an increase in the non-relaxable population. Above 10% Cholesterol/14:0 Diether PC ratio vesicles' interphase present an environment around Laurdan molecules similar to that corresponding to ester PC.

The Attraction of Water for Itself at Hydrophobic Quartz Interfaces

Structural forces within aqueous water at a solid interface can significantly change surface reactivity and the affinity of solutes toward it. We show using molecular dynamics simulations how hydrophilic and hydrophobic quartz surfaces perturb the orientational structure of aqueous water, ultimately strengthening dipolar forces between molecules in proximity to the interface. When derived as a function of distance from each surface, it was found that both surfaces indirectly enhance the long-range dipolar attraction of water for itself toward the interfacial region. This was found to be longer-ranged for water molecules solvating the hydrophobic surface than those solvating the hydrophilic surface, with a range of up to 2.5 nm from the hydrophobic surface. Our results give direct quantification of surface-induced changes in solvent-solvent attraction, ultimately providing a counterintuitive addition to the balance of hydrophobic forces at aqueous-solid interfaces.

A structural indicator for water built upon potential energy considerations

We introduce a parameter-free structural indicator to classify local environments of water molecules in stable and supercooled liquid states, which reveals a clear two-peak distribution of local properties. The majority of molecules are tetrahedrally coordinated (T molecules), via low-energy hydrogen bonds. The minority component, whose relative concentration decreases with a decrease in the temperature at constant pressure, is characterized by prevalently three-coordinated molecules, giving rise to a distorted local network around them (D molecules). The inter-conversion between T and D molecules explains the increasing specific heat at constant pressure on cooling. The local structure around a T molecule resembles the one found experimentally in low-density amorphous ice (a network structure mostly composed by T molecules), while the local structure around a D molecule is reminiscent of the structural properties of high-density amorphous ice (a network structure composed by a mixture of T and D molecules).

Influence of surface hydrophilicity and hydration on the rotational relaxation of supercooled water on graphene oxide surfaces

The presence of a bulk water film influences the dynamical transitions of supercooled water on graphene oxide surfaces.

Structural features of high-local-density water molecules: Insights from structure indicators based on the translational order between the first two molecular shells

The two-liquids scenario for liquid water assumes the existence of two competing preferential local molecular structural states characterized by either low or high local density. While the former is expected to present good local order thus involving privileged structures, the latter is usually regarded as conforming a high-entropy unstructured state. A main difference in the local arrangement of such "classes" of water molecules can be inferred from the degree of translational order between the first and second molecular shells. This is so, since the low-local-density molecules present a clear gap between the first two shells while in the case of the high-local-density ones, one or more molecules from the second shell have collapsed toward the first one, thus populating the intershell region. Some structural indicators, like the widely employed local structure index and the recently introduced ζ index, have been devised precisely on the basis of this observation, being successful in detecting well-structured low-local-density molecules. However, the nature of the high-local-density state has been mainly disregarded over the years. In this work we employ molecular dynamics simulations for two water models (the extended simple point charge model and the five-site model) at the liquid and supercooled regimes combined with the inherent dynamics approach (energy minimizations of the instantaneous configurations) in order to both rationalize the detailed structural and topological information that these indicators provide and to advance in our understanding of the high-density state.

Molecular Shape and the Hydrophobic Effect

This review focuses on papers published since 2000 on the topic of the properties of solutes in water. More specifically, it evaluates the state of the art of our understanding of the complex relationship between the shape of a hydrophobe and the hydrophobic effect. To highlight this, we present a selection of references covering both empirical and molecular dynamics studies of small (molecular-scale) solutes. These include empirical studies of small molecules, synthetic hosts, crystalline monolayers, and proteins, as well as in silico investigations of entities such as idealized hard and soft spheres, small solutes, hydrophobic plates, artificial concavity, molecular hosts, carbon nanotubes and spheres, and proteins.

A modeling study of methane hydrate decomposition in contact with the external surface of zeolites

Methane hydrate dissociates on the external surface of siliceous zeolites with methane absorbed by the solid and water forming a liquid-like phase.

Structure and dynamics of high- and low-density water molecules in the liquid and supercooled regimes

By combining the local structure index with potential energy minimisations we study the local environment of the water molecules for a couple of water models, TIP5P-Ew and SPC/E, in order to characterise low- and high-density "species". Both models show a similar behaviour within the supercooled regime, with two clearly distinguishable populations of unstructured and structured molecules, the fraction of the latter increasing with supercooling. Additionally, for TIP5P-Ew, we find that the structured component vanishes quickly at the normal liquid regime (above the melting temperature). Thus, while SPC/E provides a fraction of structured molecules similar to that found in X-ray experiments, we show that TIP5P-Ew underestimates such value. Moreover, unlike SPC/E, we demonstrate that TIP5P-Ew does not follow the linear dependence of the logarithm of the structured fraction with inverse temperature, as predicted by the two-order parameter model. Finally, we link structure to dynamics by showing that there exists a strong correlation between structural fluctuation and dynamics in the supercooled state with spatial correlations in both static and dynamic quantities.

Characterization of the Local Structure in Liquid Water by Various Order Parameters

A wide range of geometric order parameters have been suggested to characterize the local structure of liquid water and its tetrahedral arrangement, but their respective merits have remained elusive. Here, we consider a series of popular order parameters and analyze molecular dynamics simulations of water, in the bulk and in the hydration shell of a hydrophobic solute, at 298 and 260 K. We show that these parameters are weakly correlated and probe different distortions, for example the angular versus radial disorders. We first combine these complementary descriptions to analyze the structural rearrangements leading to the density maximum in liquid water. Our results reveal no sign of a heterogeneous mixture and show that the density maximum arises from the depletion in interstitial water molecules upon cooling. In the hydration shell of the hydrophobic moiety of propanol, the order parameters suggest that the water local structure is similar to that in the bulk, with only a very weak depletion in ordered configurations, thus confirming the absence of any iceberg-type structure. Finally, we show that the main structural fluctuations that affect water reorientation dynamics in the bulk are angular distortions, which we explain by the jump hydrogen-bond exchange mechanism.

Hydration and Nanoconfined Water: Insights from Computer Simulations

The comprehension of the structure and behavior of water at interfaces and under nanoconfinement represents an issue of major concern in several central research areas like hydration, reaction dynamics and biology. From one side, water is known to play a dominant role in the structuring, the dynamics and the functionality of biological molecules, governing main processes like protein folding, protein binding and biological function. In turn, the same principles that rule biological organization at the molecular level are also operative for materials science processes that take place within a water environment, being responsible for the self-assembly of molecular structures to create synthetic supramolecular nanometrically-sized materials. Thus, the understanding of the principles of water hydration, including the development of a theory of hydrophobicity at the nanoscale, is imperative both from a fundamental and an applied standpoint. In this work we present some molecular dynamics studies of the structure and dynamics of water at different interfaces or confinement conditions, ranging from simple model hydrophobic interfaces with different geometrical constraints (in order to single out curvature effects), to self-assembled monolayers, proteins and phospholipid membranes. The tendency of the water molecules to sacrifice the lowest hydrogen bond (HB) coordination as possible at extended interfaces is revealed. This fact makes the first hydration layers to be highly oriented, in some situations even resembling the structure of hexagonal ice. A similar trend to maximize the number of HBs is shown to hold in cavity filling, with small subnanometric hydrophobic cavities remaining empty while larger cavities display an alternation of filled and dry states with a significant inner HB network. We also study interfaces with complex chemical and geometrical nature in order to determine how different conditions affect the local hydration properties. Thus, we show some results for protein hydration and, particularly, some preliminary studies on membrane hydration. Finally, calculations of a local hydrophobicity measure of relevance for binding and self-assembly are also presented. We then conclude with a few words of further emphasis on the relevance of this kind of knowledge to biology and to the design of new materials by highlighting the context-dependent and non-additive nature of different non-covalent interactions in an aqueous nanoenvironment, an issue that is usually greatly overlooked.

Protein packing defects "heat up" interfacial water

Ligands must displace water molecules from their corresponding protein surface binding site during association. Thus, protein binding sites are expected to be surrounded by non-tightly-bound, easily removable water molecules. In turn, the existence of packing defects at protein binding sites has been also established. At such structural motifs, named dehydrons, the protein backbone is exposed to the solvent since the intramolecular interactions are incompletely wrapped by non-polar groups. Hence, dehydrons are sticky since they depend on additional intermolecular wrapping in order to properly protect the structure from water attack. Thus, a picture of protein binding is emerging wherein binding sites should be both dehydrons rich and surrounded by easily removable water. In this work we shall indeed confirm such a link between structure and dynamics by showing the existence of a firm correlation between the degree of underwrapping of the protein chain and the mobility of the corresponding hydration water molecules. In other words, we shall show that protein packing defects promote their local dehydration, thus producing a region of "hot" interfacial water which might be easily removed by a ligand upon association.

Temperature dependence of the structure of protein hydration water and the liquid-liquid transition

We study the temperature dependence of the structure and orientation of the first hydration layers of the protein lysozyme and compare it with the situation for a model homogeneous hydrophobic surface, a graphene sheet. We show that in both cases these layers are significantly better structured than bulk water. The geometrical constraint of the interface makes the water molecules adjacent to the surface lose one water-water hydrogen bond and expel the fourth neighbors away from the surface, lowering local density. We show that a decrease in temperature improves the ordering of the hydration water molecules, preserving such a geometrical effect. For the case of graphene, this favors an ice Ih-like local structuring, similar to the water-air interface but in the opposite way along the c axis of the basal plane (while the vicinal water molecules of the air interface orient a hydrogen atom toward the surface, the oxygens of the water molecules close to the graphene plane orient a lone pair in such a direction). In turn, the case of the first hydration layers of the lysozyme molecule is shown to be more complicated, but still displaying signs of both kinds of behavior, together with a tendency of the proximal water molecules to hydrogen bond to the protein both as donors and as acceptors. Additionally, we make evident the existence of signatures of a liquid-liquid transition (Widom line crossing) in different structural parameters at the temperature corresponding to the dynamic transition incorrectly referred to as "the protein glass transition."

Behavior of water in contact with model hydrophobic cavities and tunnels and carbon nanotubes

By means of molecular dynamics simulations we analyze the behavior of water in contact with model hydrophobic cavities and tunnels. We study the hydration and filling propensity of cavities and tunnels carved in alkane monolayers and, for comparison, we also study single-walled carbon nanotubes of similar size. Our results will determine the dependence of the filling propensity as a function of cavity size while revealing the dynamical nature of the process with alternation of filled and dry states. Concerning the tunnels built across the monolayer, we shall show that the minimum diameter in order to get filled is about twice as large as that for the carbon nanotubes, thus evidencing a more hydrophobic behavior. The existence of water-water hydrogen bonds, a necessary condition for penetration, will also be made evident.

Quantitative investigation of the two-state picture for water in the normal liquid and the supercooled regime

Several evidences have helped to establish the two-state nature of liquid water. Thus, within the normal liquid and supercooled regimes water has been shown to consist of a mixture of well-structured, low-density molecules and unstructured, high-density ones. However, quantitative analyses have faced the burden of unambiguously determining both the presence and the fraction of each kind of water "species". A recent approach by combining a local structure index with potential-energy minimisations allows us to overcome this difficulty. Thus, in this work we extend such study and employ it to quantitatively determine the fraction of structured molecules as a function of temperature for different densities. This enables us to validate predictions of two-state models.

Single-particle and collective dynamics of methanol confined in carbon nanotubes: a computer simulation study

We present the results of computer simulations of methanol confined in carbon nanotubes. Different levels of confinement were identified as a function of the nanotube radius and characterized using a pair-distribution function adapted to the cylindrical geometry of these systems. Dynamical properties of methanol were also analysed as a function of the nanotube size, both at the level of single-particle and collective properties. We found that confinement in narrow carbon nanotubes strongly affects the dynamical properties of methanol with respect to the bulk phase, due to the strong interaction with the carbon nanotube. In the other cases, confined methanol shows properties quite similar to those of the bulk phase. These phenomena are related to the peculiar hydrogen bonded network of methanol and are compared to the behaviour of water confined in similar conditions. The effect of nanotube flexibility on the dynamical properties of confined methanol is also discussed.

Sub-nanoscale surface ruggedness provides a water-tight seal for exposed regions in soluble protein structure

Soluble proteins must maintain backbone hydrogen bonds (BHBs) water-tight to ensure structural integrity. This protection is often achieved by burying the BHBs or wrapping them through intermolecular associations. On the other hand, water has low coordination resilience, with loss of hydrogen-bonding partnerships carrying significant thermodynamic cost. Thus, a core problem in structural biology is whether natural design actually exploits the water coordination stiffness to seal the backbone in regions that are exposed to the solvent. This work explores the molecular design features that make this type of seal operative, focusing on the side-chain arrangements that shield the protein backbone. We show that an efficient sealing is achieved by adapting the sub-nanoscale surface topography to the stringency of water coordination: an exposed BHB may be kept dry if the local concave curvature is small enough to impede formation of the coordination shell of a penetrating water molecule. Examination of an exhaustive database of uncomplexed proteins reveals that exposed BHBs invariably occur within such sub-nanoscale cavities in native folds, while this level of local ruggedness is absent in other regions. By contrast, BHB exposure in misfolded proteins occurs with larger local curvature promoting backbone hydration and consequently, structure disruption. These findings unravel physical constraints fitting a spatially dependent least-action for water coordination, introduce a molecular design concept, and herald the advent of water-tight peptide-based materials with sufficient backbone exposure to remain flexible.