Hydrogen Bond Network Of Water Research Articles

Structure, Dynamics, and Some Properties of Water

Development of ideas of liquid water structure since the end of the 19th century is briefly reviewed. According to the modern concepts based on experimental data and computer simulation, there is a three-dimensional hydrogen bond network in water. The structural and dynamic inhomogeneity of this network is analyzed in detail.

Hydrogen-bond Network of Water and Irradiation Effects

Results obtained in nonempirical simulations of neutral and positively charged (H2O)n water clusters with n up to 20 in the ground and excited electronic states carried out with the use of the second order Moller–Plesset perturbation theory and configuration interaction method with single and double excitations form the basis for the analysis of diverse processes promoted by the irradiation of water specimens with near and mid-range ultraviolet light with an emphasis on production of radical particles. Ionization of local H‑bonded domains results in the formation of hydronium cations and hydroxyl radicals. Concurrently, the electronic excitation and the ionization followed by the recombination of cations with hydrated electrons are shown to cause the appearance of hydrogen atoms and OH radicals.

Water Networks and Allosteric Scaffolds ‐ What Does Water Have to do with Protein Dynamics?

The thermophilic enzyme Fluoroacetate Dehalogenase (FAcD) has been well characterized by crystallography and NMR. FAcD (RPA1163) is a homodimer alpha/beta hydrolase that breaks down haloacetates (including fluoroacetate, iodoacetate, and chloroacetate) into glycolate and a halogen ion. FAcD achieves this by half‐of‐sites activity, where the homodimer adopts a rare asymmetric state that is primed to capture substrate which must then diffuse along an 11 Å cavity before engaging the active site and adopting the Michaelis intermediate. This triggers release of ~30 bound water molecules, thereby entropically favouring the forward reaction. FAcD is thus an ideal model system to pursue paradigm shifting questions regarding allostery, interprotomer communication, and the role of hydrogen bonded water networks in catalysis ‐ all from an ensemble perspective. Here we examine how deuterium water (D2O) changes the dynamic and allosteric mechanisms of this system. Compared to water, D2O results in an increase in viscosity and has stronger hydrogen bonds. Through 19F NMR kinetic experiments we determine that despite the higher viscosity enzyme activity is increased in the D2O environment. Additionally, 19F NMR experiments reveal increased dynamics in D2O. This provides key insight into discrete hydrogen‐bonded water networks that are key to stabilization of allosteric processes associated with the reaction coordinate.Support or Funding InformationNatural Sciences and Engineering Research Council (NSERC)

Temperature Dependence of X-ray-Induced Auger Processes in Liquid Water.

Auger spectroscopy has previously been used to study changes in the hydrogen bond network in liquid water, but to the best of our knowledge it has not been used to track such changes as a function of temperature. We show Auger spectroscopy to reflect the weakening of the hydrogen bond network upon heating. This shows that the radiation response of water, i.e., the relative propensity of the different processes occurring after radiation exposure, including femtosecond proton dynamics, depends on the temperature of the system. This proof-of-principle study further demonstrates the suitability of the technique to help elucidate information on the intermolecular structure of liquids such as water, opening the door to further temperature-dependent studies.

Self-assembly Processes in Hydrated Montmorillonite by FTIR Investigations.

Experimental findings obtained by FTIR and Raman spectroscopies on montmorillonite-water mixtures at three concentration values are presented. To get some insight into the hydrogen bond network of water within the montmorillonite network, FTIR and Raman spectra have been collected as a function of time and then analyzed following two complementary approaches: An analysis of the intramolecular OH stretching mode in the spectral range of 2700–3900 cm−1 in terms of two Gaussian components, and an analysis of the same OH stretching mode by wavelet cross-correlation. The FTIR and Raman investigations have been carried as a function of time for a montmorillonite-water weight composition (wt%) of 20–80%, 25–75%, and 35–65%, until the dehydrated state where the samples appear as a homogeneous rigid layer of clay. In particular, for both the FTIR and Raman spectra, the decomposition of the OH stretching band into a “closed” and an “open” contribution and the spectral wavelet analysis allow us to extract quantitative information on the time behavior of the system water content. It emerges that, the total water contribution inside the montmorillonite structure decreases as a function of time. However, the relative weight of the ordered water contribution diminishes more rapidly while the relative weight of the disordered water contribution increases, indicating that a residual water content, characterized by a highly structural disorder, rests entrapped in the montmorillonite layer structure for a longer time. From the present study, it can be inferred that the montmorillonite dehydration process promotes the layer self-assembly.

Tumbling with a limp: local asymmetry in water's hydrogen bond network and its consequences.

Ab initio molecular dynamics simulations of liquid water under equilibrium ambient conditions, together with a novel energy decomposition analysis, have recently shown that a substantial fraction of water molecules exhibit a significant asymmetry between the strengths of the two donor and/or the two acceptor interactions. We refer to this recently unraveled aspect as the "local asymmetry in the hydrogen bond network". We discuss how this novel aspect was first revealed, and provide metrics that can be consistently employed on simulated water trajectories to quantify this local heterogeneity in the hydrogen bond network and its dynamics. We then discuss the static aspects of the asymmetry, pertaining to the frozen geometry of liquid water at any given instant of time and the distribution of hydrogen bond strengths therein, and also its dynamic characteristics pertaining to how fast this asymmetry decays and the kinds of molecular motions responsible for this decay. Following this we discuss the spectroscopic manifestations of this asymmetry, from ultrafast X-ray absorption spectra to infrared spectroscopy and down to the much slower terahertz regime. Finally, we discuss the implications of these findings in a broad context and their relation to the current notions about the structure and dynamics of liquid water.

Understanding alcohol aggregates and the water hydrogen bond network towards miscibility in alcohol solutions: graph theoretical analysis.

Under ambient conditions, methanol and ethanol are miscible in water at all concentrations, while n-butanol is partially miscible. This is the first study to quantitatively examine the miscibility of butanol and compare with miscible alcohols by employing molecular dynamics simulations and graph theoretical analysis of three water-alcohol mixtures at various concentrations. We show how distinct alcohol aggregates are formed, thereby affecting the water structure, which established the relationship between the morphological structure of the aggregates and the miscibility of the alcohol in aqueous solution. The aggregates of methanol and ethanol in highly concentrated solutions form an extended H-bond network that intertwines well with the H-bond network of water. n-Butanol tends to self-associate and form large aggregates, while such aggregates are segregated from water. Graph theoretical analysis revealed that the alcohol aggregates of methanol and ethanol solutions have a morphological structure different from that of n-butanol, although there is no significant difference in morphology between the three pure alcohols. These two distinct alcohol aggregates are classified as water-compatible and water-incompatible depending upon their interaction with the water H-bond network, and their effect on the water structure was investigated. Our study reveals that the water-compatible network of alcohol aggregates in methanol and ethanol solutions disrupts the water H-bond networks, while the water-incompatible network of n-butanol aggregates does not considerably alter the water structure, which is consistent with the experimental results. Furthermore, we propose that miscible alcohols form water-compatible networks in binary aqueous systems while partially miscible alcohols form water-incompatible networks. The bifurcating hypothesis on the alcohol aggregation behavior in liquid water is of critical use to understand the fundamental issues such as solubility and phase separation in solution systems.

Structure and solvation of confined water and water-ethanol clusters within microporous Brønsted acids and their effects on ethanol dehydration catalysis.

Aqueous-phase reactions within microporous Brønsted acids occur at active centers comprised of water-reactant-clustered hydronium ions, solvated within extended hydrogen-bonded water networks that tend to stabilize reactive intermediates and transition states differently. The effects of these diverse clustered and networked structures were disentangled here by measuring turnover rates of gas-phase ethanol dehydration to diethyl ether (DEE) on H-form zeolites as water pressure was increased to the point of intrapore condensation, causing protons to become solvated in larger clusters that subsequently become solvated by extended hydrogen-bonded water networks, according to in situ IR spectra. Measured first-order rate constants in ethanol quantify the stability of SN2 transition states that eliminate DEE relative to (C2H5OH)(H+)(H2O) n clusters of increasing molecularity, whose structures were respectively determined using metadynamics and ab initio molecular dynamics simulations. At low water pressures (2-10 kPa H2O), rate inhibition by water (-1 reaction order) reflects the need to displace one water by ethanol in the cluster en route to the DEE-formation transition state, which resides at the periphery of water-ethanol clusters. At higher water pressures (10-75 kPa H2O), water-ethanol clusters reach their maximum stable size ((C2H5OH)(H+)(H2O)4-5), and water begins to form extended hydrogen-bonded networks; concomitantly, rate inhibition by water (up to -3 reaction order) becomes stronger than expected from the molecularity of the reaction, reflecting the more extensive disruption of hydrogen bonds at DEE-formation transition states that contain an additional solvated non-polar ethyl group compared to the relevant reactant cluster, as described by non-ideal thermodynamic formalisms of reaction rates. Microporous voids of different hydrophilic binding site density (Beta; varying H+ and Si-OH density) and different size and shape (Beta, MFI, TON, CHA, AEI, FAU), influence the relative extents to which intermediates and transition states disrupt their confined water networks, which manifest as different kinetic orders of inhibition at high water pressures. The confinement of water within sub-nanometer spaces influences the structures and dynamics of the complexes and extended networks formed, and in turn their ability to accommodate the evolution in polarity and hydrogen-bonding capacity as reactive intermediates become transition states in Brønsted acid-catalyzed reactions.

Water Structure in the Submembrane Region of a Floating Lipid Bilayer: The Effect of an Ion Channel Formation and the Channel Blocker.

The structure of water in the submembrane region of the bilayer of DPhPC floating (fBLM) on a monolayer of 1-thio-β-d-glucose (β-Tg)-modified gold nanoparticle film was studied by the surface-enhanced infrared absorption spectroscopy (SEIRAS). SEIRAS employs surface enhancement of the mean square electric field of the photon, which is acting on a few molecular layers above the film of gold nanoparticles. Therefore, it is uniquely suited to probe water molecules in the submembrane region and provides unique information concerning the structure of the hydrogen bond network of water surrounding the lipid bilayer. The IR spectra indicated that water with a strong hydrogen network is separating the membrane from the gold surface. This water is more ordered than the water in the bulk. When alamethicin, a peptide forming ion channels, is inserted into the membrane, the network is only slightly loosened. The addition of amiloride, an ion channel blocker, results in a significant decrease in the amount of water in the submembrane region. The remaining water has a significantly distorted hydrogen bond network. This study provides unique information about the effect of the ion channel on water transport across the bilayer. The electrode potential has a relatively small effect on water structure in the submembrane region. However, the IR studies demonstrated that water is less ordered at positive transmembrane potentials. The present results provide significant insight into the nature of hydration of a floating lipid bilayer on the gold electrode surface.

ReaxFF molecular dynamics simulations on the structure and dynamics of electrolyte water systems at ambient temperature

ReaxFF molecular dynamics simulations have been performed to study the effect of cations Li+, Na+ and K+ and anion Cl− on the structural and dynamical properties of water, using the force field recently developed by Fedkin and co-workers. The structural relationship of ion and water has been analyzed from the radial distribution function and angular distribution. Comparisons of ReaxFF angle variation of ions and water within the first solvation shell were made and found to be in good agreement with literature. The disruption of hydrogen bond network of water by ions is elucidated by ion-water residence times, water-water hydrogen bond dynamics and reorientational dynamics. ReaxFF diffusion coefficient and residence times of electrolyte water system were compared with ab initio and non-reactive potentials to analyze the difference in dynamics. We gained insight into the ion interaction with water and how it can accelerate or decelerate water dynamics. ReaxFF outlines the formation and dissolution of metal hydroxides and metal chlorides over the course of simulation to explain the diffusion dynamics of water in salt solutions, allowing us to elucidate the impact of concentration on the self-diffusivity of water and ions in solutions, and to reveal that this effect always decreases the mobility and is not at all ion-specific. The obtained results have opened new opportunities to extend the ReaxFF methodology towards systems involving electrolytes.

Characterization of Reverse Micelles Formulated with the Ionic-Liquid-like Surfactant Bmim-AOT and Comparison with the Traditional Na-AOT: Dynamic Light Scattering, 1H NMR Spectroscopy, and Hydrolysis Reaction of Carbonate as a Probe.

The present study investigated how the presence of butylmethylimidazolium cation (bmim+) alters the interfacial properties of reverse micelles (RMs) created with the ionicliquid-like surfactant 1-butyl-3-methylimidazolium 1,4-bis-2-ethylhexylsulfosuccinate (bmim-AOT), in comparison to sodium 1,4-bis-2-ethylhexylsulfosuccinate (Na-AOT) RMs, employing dynamic light scattering (DLS) and 1H NMR techniques. Moreover, through the hydrolysis reaction of bis(4-nitrophenyl)carbonate inside both RMs as reaction probe, interfacial properties changes were explored in more detail. The kinetic solvent isotope effect was also analyzed. Micellar systems were formed using n-heptane as external nonpolar solvent and water as the polar component. According to the DLS studies, water is encapsulated inside the organized media; however, a different tendency is observed depending on the cationic component of the surfactant. For Na-AOT system, the results suggest that the micellar shapes are probably spherical, while in the case of bmim-AOT, a transition from ellipsoidal to spherical micelles could be occurring when water is added. 1H NMR data show that water is structured differently when Na+ cation is replaced by bmim+; in bmim-AOT RMs, the interaction of water with the surfactant is weaker and the water hydrogen-bonding network is less disturbed than in Na-AOT RMs. Kinetic studies reveal that the hydrolysis reaction in bmim-AOT RMs was much more favorable in comparison to Na-AOT RMs. In addition, when water content decreases in bmim-AOT RMs, the hydrolysis reaction rate increases and the solvent isotope effect remains constant, while for Na-AOT solutions, both the reaction rate and the solvent isotope effect decrease. Our results indicate that bmim+ cation would be located in the surfactant layer in such a way the negative charge density in the interface is less than that in Na-AOT RMs, and the reaction is more favorable. Additionally, as 1H NMR studies reveal, the interfacial water molecules would be more available in bmim-AOT RMs to participate in the nucleophilic attack. Therefore, the present study evidences how the replacement of Na+ counterion by bmim+ alters the composition of the interface of AOT RMs.

OH radical in water from ab initio molecular dynamics simulation employing hybrid functionals

This work presents for the first time ab initio molecular dynamics simulations for the OH⋆-(H2O)n cluster with n = 0–5 and the OH radical in the bulk phase, using B3LYP as a functional. Furthermore, for OH⋆-w31, simulations with PBE0 and HSE03 are also investigated. In all systems, the OH radical is a stronger hydrogen bond donor than acceptor; a stronger hydrogen bond donor than water and a weaker hydrogen bond acceptor than water. Radial distribution functions (RDFs) reveal that for all systems, neither a hemibond between radical and water nor hydrogen abstraction is present. Comparisons with past simulations indicate that BLYP leads to artifacts, such as overstructuring of water in OH⋆-w31 and the hemibonded structure. In order to have strong hydrogen bonds with an extensive hydrogen bond network, at least four water molecules are necessary. RDFs as well as continuous dimer existence autocorrelation functions show that the OH radical is not disrupting the hydrogen bond network of water. In the bulk phase, the acceptor interaction is a very low probable interaction, whereas in the gas phase, it has a higher probability. The orientation of the water molecule around the OH radical is in the bulk liquid phase much less and in the gas phase enhanced, especially for the OH radical acting as a hydrogen bond donor toward one water molecule. PBE0 results for OH⋆-w31 in a strong hydrogen bond donor interaction compared to HSE03 and B3LYP, which has the weakest interaction. HSE03 leads to strong O–H interactions in OH⋆-w31, followed by PBE0 and B3LYP.

Dynamics of hydration water in gelatin and hyaluronic acid hydrogels.

We employed broadband dielectric spectroscopy (BDS), for the investigation of the water dynamics in partially hydrated hyaluronic acid (HA), and gelatin (Gel), enzymatically crosslinked hydrogels, in the water fraction ranges [Formula: see text]. Our results indicate that at low hydrations ([Formula: see text]), where the dielectric response of the hydrogels is identical during cooling and heating, water plasticizes strongly the polymeric matrix and is organized in clusters giving rise to [Formula: see text]-process, secondary water relaxation and to an additional slower relaxation process. This later process has been found to be related with the dc charge conductivity and can be described in terms of the conduction current relaxation mechanism. At slightly higher hydrations, however, always below the hydration level where ice is formed during cooling, we have recorded in HA hydrogel a strong water dielectric relaxation process, [Formula: see text], which has Arrhenius-like temperature dependence and large time scale resembling relaxation processes recorded in bulk low density amorphous solid water structures. This relaxation process shows a strong-to-fragile transition at [Formula: see text]C and our data suggest that the VTF-like process recorded at [Formula: see text]C is controlled by the same molecular process like long range charge transport. In addition, our data imply that the crossover temperature is related with the onset of structural rearrangements (increase in configurational entropy) of the macromolecules. In partially crystallized hydrogels ([Formula: see text]) HA exhibits at low temperatures the ice dielectric process consistent with the bulk hexagonal ice, whereas Gel hydrogel exhibits as main low temperature process a slow relaxation process that refers to open tetrahedral structures of water similar to low density amorphous ice structures and to bulk cubic ice. Regarding the water secondary relaxation processes, we have shown that the [Formula: see text]-process and the [Formula: see text] process are activated in water hydrogen bond networks with different structures.

Analysis of hydration water around human serum albumin using near-infrared spectroscopy

Hydration plays a fundamental role in maintaining the structure and function of proteins. To get a generalized picture of hydrogen bond network of water surrounding human serum albumin (HSA), near-infrared (NIR) spectroscopy was adopted to explore the hydration induced structural changes of water with HSA concentration from 0.015 to 0.746 mmol/L. As HSA concentration increases, there was a nonlinear change in molar extinction coefficients inconsistent with Beer-Lambert law indicating the changes of hydration water induced by HSA and subsequently confirmed by the hydration number. The decreasing of hydration number with HSA concentration was explained by an overlapping hydration layer model. Resolution of the difference spectra with McCabe-Fisher method and aquaphotomics clearly differentiated the hydrogen bonding of hydration water around HSA. A comparison of resolved hydration spectra highlights that free hydrogen bonded water is present in the hydration layer. As the concentration increased, a more ordered hydrogen bonded water network forms around HSA. These measurements provide unique insight into the relationship between the hydration water and HSA, which is important for understanding the dynamics of protein solution in many biochemical processes, and may serve as a basis for the purification in production.

A combined experimental and theoretical study of radon solubility in fat and water

Radon is a radioactive noble gas that can enter the human body, thus increasing the risk of lung cancer. But it is also used for treatment of various ailments, most notably rheumatoid arthritis. The accumulation of radon differs between tissues, with particularly high concentrations in fat tissue. To understand the underlying mechanisms, a combination of γ-spectroscopy and molecular dynamics simulations were performed, to study the accumulation of radon gas in contact with several liquids (water, fatty acids). The solubilities, specific for a defined radon activity concentration, are in good agreement and differ by two orders of magnitude between water and fat, caused by radon disrupting the hydrogen bond network of water. In contrast, the energy cost of introducing radon atoms into fat is low due to the dispersive interaction between radon and fat, which is a non-polar solvent. This correlation was also explicitly demonstrated in our simulations by changing the polarization of the solvent.

Enhancement of the local asymmetry in the hydrogen bond network of liquid water by an ultrafast electric field pulse

Condensed phase electron decomposition analysis based on density functional theory has recently revealed an asymmetry in the hydrogen-bond network in liquid water, in the sense that a significant population of water molecules are simultaneously donating and accepting one strong hydrogen-bond and another substantially weaker one. Here we investigate this asymmetry, as well as broader structural and energetic features of water’s hydrogen-bond network, following the application of an intense electric field square pulse that invokes the ultrafast reorientation of water molecules. We find that the necessary field-strength required to invoke an ultrafast alignment in a picosecond time window is on the order of 108 Vm−1. The resulting orientational anisotropy imposes an experimentally measurable signature on the structure and dynamics of the hydrogen-bond network, including its asymmetry, which is strongly enhanced. The dependence of the molecular reorientation dynamics on the field-strength can be understood by relating the magnitude of the water dipole–field interaction to the rotational kinetic energy, as well as the hydrogen-bond energy.

Kinetics of Aqueous Media Reactions via Ab Initio Enhanced Molecular Dynamics: The Case of Urea Decomposition.

Aqueous solutions provide a medium for many important reactions in chemical synthesis, industrial processes, environmental chemistry, and biological functions. It is an accepted fact that aqueous solvents can be direct participants in the reaction process and not act only as simple passive dielectrics. Assisting water molecules and proton wires are thus essential for the efficiency of many reactions. Here, we study the decomposition of urea into ammonia and isocyanic acid by means of enhanced ab initio molecular dynamics simulations. We highlight the role of the solvent molecules and their interactions with the reactants providing a proper description of the reaction mechanism and how the water hydrogen-bond network affects the reaction dynamics. Reaction free energy and rates have been calculated taking into account this important effect.

Proton-Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel.

The influenza A M2 protein is an acid-activated proton channel responsible for acidification of the inside of the virus, a critical step in the viral life cycle. This channel has four central histidine residues that form an acid-activated gate, binding protons from the outside until an activated state allows proton transport to the inside. While previous work has focused on proton transport through the channel, the structural and dynamic changes that accompany proton flux and enable activation have yet to be resolved. In this study, extensive Multiscale Reactive Molecular Dynamics simulations with explicit Grotthuss-shuttling hydrated excess protons are used to explore detailed molecular-level interactions that accompany proton transport in the +0, + 1, and +2 histidine charge states. The results demonstrate how the hydrated excess proton strongly influences both the protein and water hydrogen-bonding network throughout the channel, providing further insight into the channel's acid-activation mechanism and rectification behavior. We find that the excess proton dynamically, as a function of location, shifts the protein structure away from its equilibrium distributions uniquely for different pH conditions consistent with acid-activation. The proton distribution in the xy-plane is also shown to be asymmetric about the channel's main axis, which has potentially important implications for the mechanism of proton conduction and future drug design efforts.

Intramolecular OH stretching analysis of hydrated lysozyme in presence of trehalose by IR spectroscopy

The present work reports the analysis of the intramolecular OH stretching band obtained by InfraRed spectroscopy measurements. In order to characterize the effect of trehalose on the hydration properties of lysozyme the so-called two-state model is adopted for the analysis of the intramolecular OH stretching band. This latter assumes that, provided that the trehalose OH stretching contribution is subtracted, water molecules can be partitioned into two different states of inter-molecular bonding: molecules with two OH groups both hydrogen-bonded within a tetrahedral network, and molecules with one or two dangling OH groups. What emerges from this study is that trehalose significantly influences the hydrogen bond network of water and its temperature behaviour. Such a result confirms that the trehalose induced strengthening of the hydrogen-bond network leads to a stabilization of the lysozyme structure. Moreover, the analysis of the spectra temperature dependence shows a trehalose-induced higher thermal restraint of the lysozyme-trehalose-water system in respect to the lysozyme-water mixture.

Hydrogen Bond Networks in Binary Mixtures of Water and Organic Solvents.

We here present an approach for the optical in situ characterization of hydrogen bond networks (HBNs) in binary mixtures of water and organic solvents (OSs), such as methanol, ethanol, and acetonitrile. HBNs are characterized based on (i) the analysis of experimental molar Raman spectra of the mixture, (ii) partial molar Raman spectra of the mixture constituents, and (iii) computed ideal molar Raman spectra of the mixture. Especially, the consideration of the partial molar Raman spectra provides insights into the development of hydrogen bonds of molecules of one species with their neighbors. The obtained Raman spectra are evaluated with respect to the centroid of the symmetric stretching vibration Raman signal of water and to the hydroxyl stretching vibration of alcohols. We show the influence of composition and temperature on the development of the HBN of the mixtures, the HBN of water, and the HBN of the OS molecules.