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.

Persistent Local Structural Defectiveness as an Early Time Predictor of Intermittent Glassy Relaxation Events in Supercooled Water.

To become a glass from the metastable supercooled state, a liquid experiences a dramatic dynamical slowing down within a narrow temperature window. However, the attainment of solid rigidity is not the result of breaking translational symmetry as in a crystal: the structure of the resulting amorphous solid strikingly resembles that of the liquid state. Moreover, the supercooled liquid is dynamically heterogeneous; that is, the dynamics varies by orders of magnitude from one region of the sample to another, but the establishment of the existence of strong structural differences between such regions has demanded hard efforts along the years. In this work, we focus precisely on such a structure-dynamics link for supercooled water showing that local regions with structural defectiveness are persistent during the structural relaxation of the system, hence acting as early time predictors of later intermittent glassy relaxation events.

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.

Development of new 1, 3-dihydroxyacridone derivatives as Akt pathway inhibitors in skeletal muscle cells.

In the present work, four new compounds based on the privileged structure acridone were efficiently synthesized following simple operational techniques and biologically tested on proliferative skeletal muscle cells (C2C12) and rhabdomyosarcoma cells (RD) showing no significant changes in the number of dead or viable cells at 1 µM during 24 or 48 h of treatment. Of relevance, acridone derivatives 3a-3d at 0.5 µM for 24 h effectively inhibited Akt activation in C2C12, while at 1 µM only compounds 3a and 3b have effect. RD cells showed a different response pattern. These cells treated with 3a (0.5 µM), 3b (0.5 µM) or 3d (0.5 or 1 µM) for 24 h shown significant Akt inhibition. In addition, 3a-3d assayed at 1 µM for 48 h were highly successful in inhibiting Akt phosphorylation. Finally, based on molecular docking and molecular dynamics simulations, we rationalize the experimental results mentioned above and propose that 3-phosphoinositide-dependent kinase-1 (PDK1) could be one of the molecular targets of this new series of 1, 3-dihydroxyacridone derivatives. Biological and in silico studies revealed that 3b could be considered as the most promising prototype for the development of new antitumor agents.

Biophysical interactions of phenolic acids from yerba mate tea with lipid membranes.

Yerba mate (Ilex paraguariensis) tea is a well know source of phenolic antioxidants compounds. Caffeoyl derivatives are the primary constituents that account for the antioxidant capacity of this beverage. It was proposed that the interaction of polyphenols with lipid bilayers of various cell types provides the molecular rationale for their hallmark antioxidant and anti-inflammatory activities. In this study, atomistic molecular dynamics (MD) simulations were carried out in order to outline a detailed picture of the molecular interactions between three caffeoyl acids derivatives and two different lipid bilayers. We show that the three phenolic acids are able to interact at the upper regions of lipid bilayers, confining their action to the membrane surface; moreover, the strength of these interactions relay on the probability of metabolite protonation once inserted in the bilayer.

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.

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 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.

Comparing the performance of two structural indicators for different water models while seeking for connections between structure and dynamics in the glassy regime.

In this work, we compare the performance of two structural indicators based on the degree of translational order up to the second coordination shell in three water models: SPC/E, TIP4P/2005, and TIP5P. Beyond directly contrasting their distributions for different temperatures to evidence their usefulness in estimating the fraction of structured and unstructured molecules and, when possible, their classification capability, we also correlate them with an indirect measure of structural constraint: the dynamic propensity. Furthermore, this procedure enables us to show the existence of evident correlations between structural and dynamical information. More specifically, we find that locally structured molecules display a preference for low dynamic propensity values and, more conspicuously, that locally unstructured molecules are extremely subject to high dynamic propensity. This result is particularly relevant for the supercooled regime where the establishment of firm links between the structure and dynamics has remained rather elusive since the occurrence of dynamics that vary in orders of magnitude upon supercooling usually contrast with barely noticeable overall structural changes.

Size dependence of dynamic fluctuations in liquid and supercooled water.

We study the evolution of dynamic fluctuations averaged over different space lengths and time scales to characterize spatially and temporally heterogeneous behavior of TIP4P/2005 water in liquid and supercooled states. Analyzing a 250 000 molecules simulated system, we provide evidence of the existence, upon supercooling, of a significant enhancement of spatially localized dynamic fluctuations stemming from regions of correlated mobile molecules. We show that both the magnitude of the departure from the value expected for the system-size dependence of an uncorrelated system and the system size at which such a trivial regime is finally recovered clearly increase upon supercooling. This provides a means to estimate an upper limit to the maximum length scale of influence of the regions of correlated mobile molecules. Notably, such an upper limit grows two orders of magnitude on cooling, reaching a value corresponding to a few thousand molecules at the lowest investigated temperature.

Spatiotemporal intermittency and localized dynamic fluctuations upon approaching the glass transition.

We introduce a robust approach for characterizing spatially and temporally heterogeneous behavior within a system based on the evolution of dynamic fluctuations averaged over different space lengths and timescales. We apply it to investigate the dynamics in two canonical systems as the glass transition is approached: simulated Lennard-Jones liquids and experimental dense colloidal suspensions. In both cases the onset of glassiness is marked by spatially localized dynamic fluctuations originating in regions of correlated mobile particles. By removing the trivial system size dependence we show that the spatial heterogeneity of the dynamics extends to large length scales containing tens to hundreds of particles, corresponding to the timescale of maximally non-Gaussian dynamics.

Design, synthesis and biological evaluation of 1,3-dihydroxyxanthone derivatives: Effective agents against acetylcholinesterase.

The present work concerns the rational design and development of new inhibitors of acetylcholinesterase (AChE) based on the privileged xanthone scaffold. In order to understand and rationalize the mode of action of these target structures a theoretical study was initially conducted. From the results of rational design, a new variety of amphiphilic xanthone derivatives were synthesized, structurally characterized and evaluated as potential anti-Alzheimer agents. The results showed that most of the synthesized compounds exhibited high AChE inhibitory activity at the micromolar range (IC50, 0.46-12.09µM). The synthetic xanthone 11 showed the best inhibitory effect on AChE and a molecular modeling study revealed that 11 targeted both the catalytic active site (CAS) and the peripheral anionic site (PAS) of AChE. Therefore, this compound could be considered asa potential lead compound towards new drugs for the treatment of Alzheimer's disease.

Studies on electrostatic interactions within model nano-confined aqueous environments of different chemical nature.

We study the potential of mean force for pairs of parallel flat surfaces with attractive electrostatic interactions by employing model systems functionalized with different charged, hydrophobic and hydrophilic groups. We study the way in which the local environment (hydrophobic or hydrophilic moieties) modulates the interaction between the attractive charged groups on the plates by removing or attracting nearby water and thus screening or not the electrostatic interaction. To explicitly account for the role of the solvent and the local hydrophobicity, we also perform studies in vacuo. Additionally, the results are compared to that for non-charged plates in order to single out and rationalize the non-additivity of the different non-covalent interactions. Our simulations demonstrate that the presence of neighboring hydrophobic groups promote water removal in the vicinity of the charged groups, thus enhancing charge attraction upon self-assembly. This role of the local hydrophobicity modulating electrostatic interactions is consistent with recent qualitative descriptions in the protein binding context.

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.

Hydrogen Bond Dynamic Propensity Studies for Protein Binding and Drug Design.

We study the dynamic propensity of the backbone hydrogen bonds of the protein MDM2 (the natural regulator of the tumor suppressor p53) in order to determine its binding properties. This approach is fostered by the observation that certain backbone hydrogen bonds at the p53-binding site exhibit a dynamical propensity in simulations that differs markedly form their state-value (that is, formed/not formed) in the PDB structure of the apo protein. To this end, we conduct a series of hydrogen bond propensity calculations in different contexts: 1) computational alanine-scanning studies of the MDM2-p53 interface; 2) the formation of the complex of MDM2 with the disruptive small molecule Nutlin-3a (dissecting the contribution of the different molecular fragments) and 3) the binding of a series of small molecules (drugs) with different affinities for MDM2. Thus, the relevance of the hydrogen bond propensity analysis for protein binding studies and as a useful tool to complement existing methods for drug design and optimization will be made evident.

Water populations in restricted environments of lipid membrane interphases.

We employ molecular dynamics simulations to study the hydration properties of Dipalmitoylphosphatidylcholine (DPPC) bilayers, both in the gel and the liquid crystalline states. We show that while the tight hydration centers (PO and CO moieties) are significantly hydrated in both phases, the gel-fluid transition involves significant changes at the second hydration shell, particularly at the buried region between the hydrocarbon tails. Thus, while almost no buried water population exists in the gel state below the carbonyls, this hydrophobic region becomes partially water accesible in the liquid crystalline state. We shall also show that such water molecules present a lower H-bond coordination as compared to the molecules at the primary hydration shell. This means that, while the latter are arranged in relatively compact nanoclusters (as already proposed), the buried water molecules tend to organize themselves in less compact structures, typically strings or branched strings, with a scarce population of isolated molecules. This behavior is similar to that observed in other hydration contexts, like water penetrating carbon nanotubes or model hydrophobic channels or pores, and reflects the reluctance of water to sacrifice HB coordination.

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.