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

Role of hydrogen-bond coordination defects in the structural relaxation of supercooled water

In this work, we shall study the role of threefold and fivefold coordination defects in the structure and dynamics of the hydrogen bond network of liquid water, with special emphasis on the glassy regime. A significant defect clusterization propensity will be made evident, with a prevalence of mixed pairs, that is, threefold- and fivefold-coordinated defects being first neighbors of each other. This structural analysis will enable us to determine the existence of defective and nondefective regions compatible with the high local density and low local density molecular states of liquid water, respectively. Hydrogen bond coordination defects will also be shown to promote water's structural relaxation, with the undercoordinated ones playing a main role in driving glassy relaxation dynamics. Moreover, we shall show that the three-foldcoordinated molecules together with their first neighbors present at the initial configuration act as markers of the dynamical heterogeneities that would emerge at later times commensurate with the structural relaxation of the supercooled system.

A structural determinant of the behavior of water at hydration and nanoconfinement conditions

The molecular nature of the phases that conform the two-liquid scenario is elucidated in this work in the light of a molecular principle governing water structuring, which unveils the relevance of the contraction and reorientation of the second molecular shell to allow for the existence of coordination defects in water's hydrogen bond network. In turn, such principle is shown to also determine the behavior of hydration and nanoconfined water while enabling to define conditions for wettability (quantifying hydrophobicity and predicting drying transitions), thus opening the possibility to unravel the active role of water in central fields of research.

Water at the nanoscale: From filling or dewetting hydrophobic pores and carbon nanotubes to "sliding" on graphene

In this work, we study the effect of nanoconfinement on the hydration properties of model hydrophobic pores and carbon nanotubes, determining their wetting propensity and the conditions for geometrically induced dehydration. By employing a recently introduced water structural index, we aim at two main goals: (1) to accurately quantify the local hydrophobicity and predict the drying transitions in such systems, and (2) to provide a molecular rationalization of the wetting process. In this sense, we will further discuss the number and strength of the interactions required by the water molecules to promote wetting. In the case of graphene-like surfaces, an explanation for their unexpectedly significant hydrophilicity will also be provided. On the one hand, the structural index will show that the net attraction to the dense carbon network that a water molecule experiences through several simultaneous weak interactions is sufficient to give rise to hydrophilic behavior. On the other hand, we will show that an additional effect is also at play: the hydrating water molecule is retained on the surface by a smooth exchange of such simultaneous weak interactions, as if "sliding" on graphene.

A water structure indicator suitable for generic contexts: Two-liquid behavior at hydration and nanoconfinement conditions and a molecular approach to hydrophobicity and wetting

In a recent work, we have briefly introduced a new structural index for water that, unlike previous indicators, was devised specifically for generic contexts beyond bulk conditions, making it suitable for hydration and nanoconfinement settings. In this work, we shall study this metric in detail, demonstrating its ability to reveal the existence of a fine-tuned interplay between the local structure and energetics in liquid water. This molecular principle enables the establishment of an extended hydrogen bond network, while simultaneously allowing for the existence of network defects by compensating for uncoordinated sites. By studying different water models and different temperatures encompassing both the normal liquid and the supercooled regime, this molecular mechanism will be shown to underlie the two-state behavior of bulk water. In addition, by studying functionalized self-assembled monolayers and diverse graphene-like surfaces, we shall show that this principle is also operative at hydration and nanoconfinement conditions, thus generalizing the validity of the two-liquid scenario of water to these contexts. This approach will allow us to define conditions for wettability, providing an accurate measure of hydrophobicity and a reliable predictor of filling and drying transitions. Hence, it might open the possibility of elucidating the active role of water in the broad fields of biophysics and materials science. As a preliminary step, we shall study the hydration structure and hydrophilicity of graphene-like systems (parallel graphene sheets and carbon nanotubes) as a function of the confinement dimensionality.

Turning an energy-based defect detector into a multi-molecule structural indicator for water

Recent studies have provided conclusive evidence for the existence of a liquid-liquid critical point in numerical models of water. Such a scenario implies the competition between two local molecular arrangements of different densities: a high-density liquid (HDL) and a low-density liquid (LDL). Within this context, the development of accurate structural indicators to properly characterize the two interconverting local structures is demanded. In a previous study, we introduced a reliable energy-based structural descriptor that properly discriminates water molecules into tetrahedrally arranged molecules (T molecules) and distorted molecules (D molecules). The latter constitute defects in terms of hydrogen bond (HB) coordination and have been shown to represent a minority component, even at high temperatures above the melting point. In addition, the D molecules tend to form high-quality HBs with three T molecules and to be surrounded by T and D molecules at further distances. Thus, it became evident that, while the LDL state might consist of a virtually pure T state, the HDL state would comprise mixed molecular arrangements including the D molecules. Such a need to abandon the single-molecule description requires the investigation of the degree of structural information to be incorporated in order to build an appropriate multi-molecule indicator. Hence, in this work, we shall study the effect of the local structural constraints on the water molecules in order to discriminate the different molecular arrangements into two disjoint classes. This will enable us to build a multi-molecule structural indicator for water whose performance will then be investigated within the water's supercooled regime.

Correlations between defect propensity and dynamical heterogeneities in supercooled water

A salient feature of supercooled liquids consists in the dramatic dynamical slowdown they undergo as temperature decreases while no significant structural change is evident. These systems also present dynamical heterogeneities (DH): certain molecules, spatially arranged in clusters, relax various orders of magnitude faster than the others. However, again, no static quantity (such as structural or energetic measures) shows strong direct correlations with such fast-moving molecules. In turn, the dynamic propensity approach, an indirect measure that quantifies the tendency of the molecules to move in a given structural configuration, has revealed that dynamical constraints, indeed, originate from the initial structure. Nevertheless, this approach is not able to elicit which structural quantity is, in fact, responsible for such a behavior. In an effort to remove dynamics from its definition in favor of a static quantity, an energy-based propensity has also been developed for supercooled water, but it could only find positive correlations between the lowest-energy and the least-mobile molecules, while no correlations could be found for those more relevant mobile molecules involved in the DH clusters responsible for the system's structural relaxation. Thus, in this work, we shall define a defect propensity measure based on a recently introduced structural index that accurately characterizes water structural defects. We shall show that this defect propensity measure provides positive correlations with dynamic propensity, being also able to account for the fast-moving molecules responsible for the structural relaxation. Moreover, time dependent correlations will show that defect propensity represents an appropriate early-time predictor of the long-time dynamical heterogeneity.

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.

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.

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.

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.

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).

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.

The spatial range of protein hydration

Proteins interact with their aqueous surroundings, thereby modifying the physical properties of the solvent. The extent of this perturbation has been investigated by numerous methods in the past half-century, but a consensus has still not emerged regarding the spatial range of the perturbation. To a large extent, the disparate views found in the current literature can be traced to the lack of a rigorous definition of the perturbation range. Stating that a particular solvent property differs from its bulk value at a certain distance from the protein is not particularly helpful since such findings depend on the sensitivity and precision of the technique used to probe the system. What is needed is a well-defined decay length, an intrinsic property of the protein in a dilute aqueous solution, that specifies the length scale on which a given physical property approaches its bulk-water value. Based on molecular dynamics simulations of four small globular proteins, we present such an analysis of the structural and dynamic properties of the hydrogen-bonded solvent network. The results demonstrate unequivocally that the solvent perturbation is short-ranged, with all investigated properties having exponential decay lengths of less than one hydration shell. The short range of the perturbation is a consequence of the high energy density of bulk water, rendering this solvent highly resistant to structural perturbations. The electric field from the protein, which under certain conditions can be long-ranged, induces a weak alignment of water dipoles, which, however, is merely the linear dielectric response of bulk water and, therefore, should not be thought of as a structural perturbation. By decomposing the first hydration shell into polarity-based subsets, we find that the hydration structure of the nonpolar parts of the protein surface is similar to that of small nonpolar solutes. For all four examined proteins, the mean number of water-water hydrogen bonds in the nonpolar subset is within 1% of the value in bulk water, suggesting that the fragmentation and topography of the nonpolar protein-water interface has evolved to minimize the propensity for protein aggregation by reducing the unfavorable free energy of hydrophobic hydration.

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.

Wrapping effects within a proposed function-rescue strategy for the Y220C oncogenic mutation of protein p53

Soluble proteins must protect their structural integrity from water attack by wrapping interactions which imply the clustering of nonpolar residues around the backbone hydrogen bonds. Thus, poorly wrapped hydrogen bonds constitute defects which have been identified as promoters of protein associations since they favor the removal of hydrating molecules. More specifically, a recent study of our group has shown that wrapping interactions allow the successful identification of protein binding hot spots. Additionally, we have also shown that drugs disruptive of protein-protein interfaces tend to mimic the wrapping behavior of the protein they replace. Within this context, in this work we study wrapping three body interactions related to the oncogenic Y220C mutation of the tumor suppressor protein p53. Our computational results rationalize the oncogenic nature of the Y220C mutation, explain the binding of a drug-like molecule already designed to restore the function of p53 and provide clues to help improve this function-rescue strategy and to apply in other drug design or re-engineering techniques.