Mechanisms of the molecular mobility of water

Reverse Micelles As Antioxidant Carriers: An Experimental and Molecular Dynamics Study

Water-in-oil microemulsions with biocompatible components were formulated to be used as carriers of natural antioxidants, such as hydroxytyrosol (HT) and gallic acid (GA). The system was composed of a mixture of natural surfactants, lecithin and monoglycerides, medium chain triglycerides, and aqueous phase. A dual approach was undertaken to study the structure and dynamics of these complicated systems. First, experimental data were collected by using adequate techniques, such as dynamic light scattering (DLS) and electron paramagnetic resonance (EPR) spectroscopy. Following this, a coarse-grained molecular dynamics (CGMD) study based on the experimental composition using the MARTINI force field was conducted. The simulations revealed the spontaneous formation of reverse micelles (RMs) starting from completely random initial conformations, underlying their enhanced thermodynamic stability. The location of the bioactive molecules, as well as the structure of the RM, were in accordance with the experimental findings. Furthermore, GA molecules were found to be located inside the water core, in contrast to the HT ones, which seem to lie at the surfactant interfacial layer. The difference in the antioxidants' molecular location was only revealed in detail from the computational analysis and explains the RM's swelling observed by GA in DLS measurements.

The origin of the Debye relaxation in liquid water and fitting the high frequency excess response

Debye relaxation in the microwave/THz region of the dielectric spectra of water is related to propagation of defects.

Water's dual nature and its continuously changing hydrogen bonds

A model is proposed for liquid water that is a continuum between the ordered state with predominantly tetrahedral coordination, linear hydrogen bonds and activated dynamics and a disordered state with a continuous distribution of multiple coordinations, multiple types of hydrogen bond, and diffusive dynamics, similar to that of normal liquids. Central to water's heterogeneous structure is the ability of hydrogen to donate to either one acceptor in a conventional linear hydrogen bond or to multiple acceptors as a furcated hydrogen. Linear hydrogen bonds are marked by slow, activated kinetics for hydrogen-bond switching to more crowded acceptors and sharp first peaks in the hydrogen-oxygen radial distribution function. Furcated hydrogens, equivalent to free, broken, dangling or distorted hydrogens, have barrierless, rapid kinetics and poorly defined first peaks in their hydrogen-oxygen radial distribution function. They involve the weakest donor in a local excess of donors, such that barrierless whole-molecule vibration rapidly swaps them between the linear and furcated forms. Despite the low number of furcated hydrogens and their transient existence, they are readily created in a single hydrogen-bond switch and free up the dynamics of numerous surrounding molecules, bringing about the disordered state. Hydrogens in the ordered state switch with activated dynamics to make the non-tetrahedral coordinations of the disordered state, which can also combine to make the ordered state. Consequently, the ordered and disordered states are both connected by diffusive dynamics and differentiated by activated dynamics, bringing about water's continuous heterogeneity.

The mechanism of the dielectric relaxation in water

The water spectra from Raman and Dielectric spectroscopies are combined to present a cohesive description of water dynamics up to the THz region.

Macro and nano scale modelling of water–water interactions at ambient and low temperature: relaxation and residence times

A method to predict magnitudes in quantitative agreement with experimental data has been devised and applied to model water–water interactions at low temperature.

Liquid water: from symmetry distortions to diffusive motion

Water deviates from tetrahedral symmetry on different scales, creating "defects" that are important for its dynamics. In this Account, I trace the manifestations of these distortions from the isolated molecule through gas-phase clusters to the liquid phase. Unlike the common depiction, an isolated water molecule has a nonsymmetric charge distribution: although its positive charge is localized at the hydrogens, the negative charge is smeared between the lone-pair sites. This creates a "negativity track" along which a positive charge may slide. Consequently, the most facile motion within the water dimer is a reorientation of the hydrogen-bond (HB) accepting molecule (known as an "acceptor switch"), such that the donor hydrogen switches from one lone pair to the other. Liquid water exhibits asymmetry between donor and acceptor HBs. Molecular dynamics simulations show that the water oxygens accepting HBs from the central molecule are spatially localized, whereas water hydrogens donating HBs to it are distributed along the negativity track. This asymmetry is manifested in a wider acceptor- versus donor-HB distribution. There is a higher probability for a water molecule to accept one (trigonal symmetry) or three HBs than to donate one or three HBs. A simple model can explain semiquantitatively how these distributions evolve by distorting perfectly tetrahedral water. Just two reactions are required: the dissociation of a HB between a double-donor donating to a double-acceptor, D(2)···A(2), followed by a switching reaction in which a HB donor rotates its hydrogen between two double-acceptor molecules. The preponderance of D(2)···A(2) dissociation events is in line with HB "anticooperativity", whereas positive cooperativity is exhibited by conditional HB distributions: a molecule with more acceptor bonds tends to have more donor bonds and vice versa. Quantum mechanically, such an effect arises from intermolecular charge transfer, but it is observed even for fixed-charge water models. Possibly, in the liquid state this is partly a collective effect, for example, a more ordered hydration shell that enhances the probability for both acceptor and donor HBs. The activation energy for liquid water self-diffusion is considerably larger than its HB strength, pointing to the involvement of collective dynamics. The remarkable agreement between the temperature dependence of the water self-diffusion coefficient and its Debye relaxation time suggests that both share the same mechanism, likely consisting of coupled rotation and translation with collective rearrangement of the environment. The auto-correlation function of a hydrogen-bonded water molecule pair is depicted quantitatively by the solution of the diffusion equation for reversible geminate recombination, up to long times where the ubiquitous t(-3/2) power law prevails. From the model, one obtains the HB dissociation and formation rate coefficients and their temperature dependence. Both have a similar activation enthalpy, suggesting rapid formation of HBs with alternate partners, perhaps by the HB switching reaction involving the trigonal site. A detailed picture of how small fluctuations evolve into large-scale molecular motions in water remains elusive. Nonetheless, our results demonstrate how the plasticity of water can be traced to its asymmetric charge distribution, with duality between tetrahedral and trigonal ligation states.

Confinement effects on monosaccharide transport in nanochannels

Transport theories based on the continuum hypothesis may not be appropriate at the nanoscale in view of surface effects. We employed molecular dynamics simulations to study the effects of confinement and concentration on diffusive transport of glucose in silica nanochannels (10 nm or smaller). We found that glucose modifies the electrical properties of nanochannels and that, below 5 nm in channel height, glucose adsorption and diffusivity are significantly reduced. With increasing concentration, the diffusivity is reduced linearly in the bulk, while it is reduced nonlinearly at the interface. The effective diffusivity reduction is related to the interface thickness, which can be 2-4 nm depending on concentration, and has an unexpected reduction at low concentrations. Results suggest that nanochannels present a one-dimensional cage environment that affects diffusivity in a fashion similar to cage-breaking diffusion. Our simulation results, consistent with the experimental observations presented here, suggest that nanoconfinement is the essential cause of the observed altered fluid diffusive transport, not accounted for by classical theories, because of coupling of confinement and concentration effects.

Nuclear-magnetic-resonance measurements reveal the origin of the Debye process in monohydroxy alcohols

Monohydroxy alcohols show a structural relaxation and at longer time scales a Debye-type dielectric peak. From spin-lattice relaxation experiments using different nuclear probes, an intermediate, slower-than-structural dynamics is identified for n-butanol. Based on these findings and on translational diffusion measurements, a model of self-restructuring, transient chains is proposed. The model is demonstrated to explain consistently the so-far puzzling observations made for this class of hydrogen-bonded glass forming liquids.

Topological hydrogen-bond definition to characterize the structure and dynamics of liquid water

A definition that equates a hydrogen bond topologically with a local energy well in the potential energy surface is used to study the structure and dynamics of liquid water. We demonstrate the robustness of this hydrogen-bond definition versus the many other definitions which use fixed, arbitrary parameters, do not account for variable molecular environments, and cannot effectively resolve transition states. Our topology definition unambiguously shows that most water molecules are double acceptors but sizable proportions are single or triple acceptors. Almost all hydrogens are found to take part in hydrogen bonds. Broken hydrogen bonds only form when two molecules try to form two hydrogen bonds between them. The double acceptors have tetrahedral geometry, lower potential energy, entropy, and density, and slower dynamics. The single and triple acceptors have trigonal and trigonal bipyramidal geometry and when considered together have higher density, potential energy, and entropy, faster dynamics, and a tendency to cluster. These calculations use an extended theory for the entropy of liquid water that takes into account the variable number of hydrogen bonds. Hydrogen-bond switching is shown to depend explicitly on the variable number of hydrogen bonds accepted and the presence of interstitial water molecules. Transition state theory indicates that the switching of hydrogen bonds is a mildly activated process, requiring only a moderate distortion of hydrogen bonds. Three main types of switching events are observed depending on whether the donor and acceptor are already sharing a hydrogen bond. The switch may proceed with no intermediate or via a bifurcated-oxygen or cyclic dimer, both of which have a broken hydrogen bond and symmetric and asymmetric forms. Switching is found to be strongly coupled to whole-molecule vibration, particularly for the more mobile single and triple acceptors. Our analysis suggests that even though water is heterogeneous in terms of the number of hydrogen bonds, the coupling between neighbors on various length and time scales brings about greater continuity in its properties.

Correlation of Static and Dynamic Heterogeneities in Supercooled Water by Means of Molecular Dynamics Simulations

The unusual increase of diffusivity of supercooled water upon compression seems to be related to the existence of at least two major distinct local structural forms: a "low-density" structure, exhibiting an almost perfect tetrahedral hydrogen bonding network, and a "high-density" structure, characterized by defects in this network. The structural changes can be measured by the "tetrahedricity parameter", describing the deviation from the ideal tetrahedron. In this paper we show that the anomalous diffusion behavior upon compression cannot only be related to the structural heterogeneities but also to dynamical heterogeneities occuring in supercooled liquid water. This is shown for translational heterogeneities which decrease with temperature and pressure. Both, static and dynamic heterogeneities can be correlated. They are substantial at low temperatures and moderate pressures and diminish with increasing temperature and pressure, respectively. Our results are based on molecular dynamics simulations of the TIP4P-Ew water model [1].

Liquid water and ices: understanding the structure and physical properties

A review of the structure and some properties of condensed phases of water is given. Since the discovery of the polymorphism of crystalline ice (beginning of the twentieth century), 15 ice modifications have been found and their structures have been determined. If we do not take into consideration proton ordering or disordering, nine distinct crystalline ice modifications in which water molecules retain their individuality are known. In the tenth, ice X, there are no H(2)O molecules. It contains ions (or atoms) of oxygen and hydrogen. The structure of all these modifications is described and information about their fields of stability and about the transition between them is given. It is emphasized that there are ice modifications which are metastable at any temperature and pressure (ices Ic, IV and XII), and many modifications can exist as metastable phases beyond their fields of stability. The ability of water to exist in metastable states is one of its remarkable properties. Several amorphous ice modifications (all of them are metastable) are known. Brief information about their properties and transitions between them is given. At the end of the 1960s the conception of the water structure as a three-dimensional hydrogen-bonded network was conclusively formed. Discovery of the polymorphism of amorphous ices awakened interest in the heterogeneity of the water network. Structural and dynamical heterogeneity of liquid water is discussed in detail. Computer simulation showed that the diffusion coefficient of water molecules in dense regions of the network is lower than in the loose regions, while an increase of density of the entire network gives rise to an increase of diffusion coefficient. This finding contradicts the conceptions associated with the primitive two-state models and can be explained from pressure dependences of melting temperature and of homogeneous nucleation temperature. A brief discussion of the picture of molecular motions in liquid water based on experiment and on computer simulation is given. This picture is still very incomplete. The most fascinating idea that was put forward during the last 20 years was the second critical point conjecture. It is still not clear whether this conjecture corresponds to reality.

Dynamics at the protein-water interface from 17O spin relaxation in deeply supercooled solutions

Most of the decisive molecular events in biology take place at the protein-water interface. The dynamical properties of the hydration layer are therefore of fundamental importance. To characterize the dynamical heterogeneity and rotational activation energy in the hydration layer, we measured the (17)O spin relaxation rate in dilute solutions of three proteins in a wide temperature range extending down to 238 K. We find that the rotational correlation time can be described by a power-law distribution with exponent 2.1-2.3. Except for a small fraction of secluded hydration sites, the dynamic perturbation in the hydration layer is the same for all proteins and does not differ in any essential way from the hydration shell of small organic solutes. In both cases, the dynamic perturbation factor is <2 at room temperature and exhibits a maximum near 262 K. This maximum implies that, at low temperatures, the rate of water molecule rotation has a weaker temperature dependence in the hydration layer than in bulk water. We attribute this difference to the temperature-independent constraints that the protein surface imposes on the water H-bond network. The free hydration layer studied here differs qualitatively from confined water in solid protein powder samples.

Simulation studies of the protein-water interface. I. Properties at the molecular resolution

We report molecular dynamics simulations of three globular proteins: ubiquitin, apo-calbindin D(9K), and the C-terminal SH2 domain of phospholipase C-gamma1 in explicit water. The proteins differ in their overall charge and fold type and were chosen to represent to some degree the structural variability found in medium-sized proteins. The length of each simulation was at least 15 ns, and larger than usual solvent boxes were used. We computed radial distribution functions, as well as orientational correlation functions about the surface residues. Two solvent shells could be clearly discerned about charged and polar amino acids. Near apolar amino acids the water density near such residues was almost devoid of structure. The mean residence time of water molecules was determined for water shells about the full protein, as well as for water layers about individual amino acids. In the dynamic properties, two solvent shells could be characterized as well. However, by comparison to simulations of pure water it could be shown that the influence of the protein reaches beyond 6 A, i.e., beyond the first two shells. In the first shell (r < or =3.5 A), the structural and dynamical properties of solvent waters varied considerably and depended primarily on the physicochemical properties of the closest amino acid side chain, with which the waters interact. By contrast, the solvent properties seem not to depend on the specifics of the protein studied (such as the net charge) or on the secondary structure element in which an amino acid is located. While differing considerably from the neat liquid, the properties of waters in the second solvation shell (3.5< r < or =6 A) are rather uniform; a direct influence from surface amino acids are already mostly shielded.

Kinetic, Thermodynamic, and Mechanistic Patterns for Free (Unbound) Cytochromec at Au/SAM Junctions: Impact of Electronic Coupling, Hydrostatic Pressure, and Stabilizing/Denaturing Additives

Combined kinetic (electrochemical) and thermodynamic (calorimetric) investigations were performed for an unbound (intact native-like) cytochrome c (CytC) freely diffusing to and from gold electrodes modified by hydroxyl-terminated self-assembled monolayer films (SAMs), under a unique broad range of experimental conditions. Our approach included: 1) fine-tuning of the charge-transfer (CT) distance by using the extended set of Au-deposited hydroxyl-terminated alkanethiol SAMs [-S-(CH(2))(n)-OH] of variable thickness (n=2, 3, 4, 6, 11); 2) application of a high-pressure (up to 150 MPa) kinetic strategy toward the representative Au/SAM/CytC assemblies (n=3, 4, 6); 3) complementary electrochemical and microcalorimetric studies on the impact of some stabilizing and denaturing additives. We report for the first time a mechanistic changeover detected for "free" CytC by three independent kinetic methods, manifested through 1) the abrupt change in the dependence of the shape of the electron exchange standard rate constant (k(o)) versus the SAM thickness (resulting in a variation of estimated actual CT range within ca. 15 to 25 A including ca. 11 A of an "effective" heme-to-omega-hydroxyl distance). The corresponding values of the electronic coupling matrix element vary within the range from ca. 3 to 0.02 cm(-1); 2) the change in activation volume from +6.7 (n=3), to approximately 0 (n=4), and -5.5 (n=6) cm(3) mol(-1) (disclosing at n=3 a direct pressure effect on the protein's internal viscosity); 3) a "full" Kramers-type viscosity dependence for k(o) at n=2 and 3 (demonstrating control of an intraglobular friction through the external dynamic properties), and its gradual transformation to the viscosity independent (nonadiabatic) regime at n=6 and 11. Multilateral cross-testing of "free" CytC in a native-like, glucose-stabilized and urea-destabilized (molten-globule-like) states revealed novel intrinsic links between local/global structural and functional characteristics. Importantly, our results on the high-pressure and solution-viscosity effects, together with matching literature data, strongly support the concept of "dynamic slaving", which implies that fluctuations involving "small" solution components control the proteins' intrinsic dynamics and function in a highly cooperative manner as far as CT processes under adiabatic conditions are concerned.

Quasielastic neutron scattering investigation of the pressure dependence of molecular motions in liquid water

We report on a high-resolution, high-statistics, quasielastic neutron scattering (QENS) experiment on liquid water, aimed at accurately measuring the pressure dependence of the single-particle dynamic response function at low wave vector transfers, namely, from 0.26 to 1.32 A(-1). High-pressure QENS data were collected along the T = 268 K isothermal path over the rather extended pressure range of 80 up to 350 MPa, a thermodynamic region so far unexplored by this microscopic technique. The analysis of the measured line shapes enabled us to draw a consistent picture of the wave vector and pressure dependences of the diffusion mechanisms in liquid water, against which the most recent models for water dynamics can be checked. In close similarity with the case of supercooled water, the relaxing-cage model was found to provide a quantitatively more accurate description of the molecular motions and their pressure evolution in liquid water.

Structure and Dynamics of Water Confined in Dimethyl Sulfoxide

We study the structure and dynamics of hydrogen-bonded complexes of H2O/D2O and dimethyl sulfoxide (DMSO) by infrared spectroscopy, NMR spectroscopy and ab initio calculations. We find that single water molecules occur in two configurations. For one half of the water monomers both OH/OD groups form strong hydrogen bonds to DMSO molecules, whereas for the other half only one of the two OH/OD groups is hydrogen-bonded to a solvent molecule. The H-bond strength between water and DMSO is in the order of that in bulk water. NMR deuteron relaxation rates and calculated deuteron quadrupole coupling constants yield rotational correlation times of water. The molecular reorientation of water monomers in DMSO is two-and-a-half times slower than in bulk water. This result can be explained by local structure behavior.

Impacts of Quantization on the Properties of Liquid Water

The results of classical and quantum simulations of liquid water over a wide range of temperatures are compared to probe the impact of quantization on the properties of liquid water. We show that, when treated quantum mechanically, water molecules have an enhanced probability of accessing nontetrahedral coordination in the local three-dimensional structure. We discuss how this enhanced probability, also called "effective tunneling", is related to the dynamics of the hydrogen-bond breaking and molecular diffusion in the liquid. We explore in detail how local molecular environments affect the manifestation of quantum effects and identify a previously unreported and apparently unique behavior of the quantum mechanical uncertainty of the water molecule as a function of temperature. The nonmonotonic behavior of the quantum mechanical uncertainty with temperature is shown to be due to the notable strength of the water-water interaction in the condensed phase and becomes further evidence of the importance of the water structure in the properties of this ubiquitous liquid.

Protein hydration dynamics in solution: a critical survey

The properties of water in biological systems have been studied for well over a century by a wide range of physical techniques, but progress has been slow and erratic. Protein hydration--the perturbation of water structure and dynamics by the protein surface--has been a particularly rich source of controversy and confusion. Our aim here is to critically examine central concepts in the description of protein hydration, and to assess the experimental basis for the current view of protein hydration, with the focus on dynamic aspects. Recent oxygen-17 magnetic relaxation dispersion (MRD) experiments have shown that the vast majority of water molecules in the protein hydration layer suffer a mere twofold dynamic retardation compared with bulk water. The high mobility of hydration water ensures that all thermally activated processes at the protein-water interface, such as binding, recognition and catalysis, can proceed at high rates. The MRD-derived picture of a highly mobile hydration layer is consistent with recent molecular dynamics simulations, but is incompatible with results deduced from intermolecular nuclear Overhauser effect spectroscopy, dielectric relaxation and fluorescence spectroscopy. It is also inconsistent with the common view of hydration effects on protein hydrodynamics. Here, we show how these discrepancies can be resolved.

Biomolecular cryocrystallography: structural changes during flash-cooling

To minimize radiation damage, crystal structures of biological macromolecules are usually determined after rapid cooling to cryogenic temperatures, some 150-200 K below the normal physiological range. The biological relevance of such structures relies on the assumption that flash-cooling is sufficiently fast to kinetically trap the macromolecule and associated solvent in a room-temperature equilibrium state. To test this assumption, we use a two-state model to calculate the structural changes expected during rapid cooling of a typical protein crystal. The analysis indicates that many degrees of freedom in a flash-cooled protein crystal are quenched at temperatures near 200 K, where local conformational and association equilibria may be strongly shifted toward low-enthalpy states. Such cryoartifacts should be most important for strongly solvent-coupled processes, such as hydration of nonpolar cavities and surface regions, conformational switching of solvent-exposed side chains, and weak ligand binding. The dynamic quenching that emerges from the model considered here can also rationalize the glass transition associated with the atomic fluctuations in the protein.