Dynamics of water studied by coherent and incoherent inelastic neutron scattering

An Exploration of the Transformation of the 8-Oxo-7,8-Dihydroguanine Radical Cation to Protonated 2-Amino-5-Hydroxy-7,9-Dihydropurine-6,8-Dione in a Base Pair

A theoretical investigation was performed to disclose the transformation mechanism of 8-oxo-7,8-dihydroguanine radical cation (8-oxoG⋅⁺ ) to protonated 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-8-oxoG) in base pair. The energy profiles for three possible pathways of the events were mapped. It is shown that direct loss of H7 from base paired 8-oxoG⋅⁺ is the only energetically favorable pathway to generate neutral radical, 8-oxoG(-H7)⋅. Further oxidation of 8-oxoG(-H7)⋅ : C to 8-oxoG(-H7)⁺  : C is exothermic. However, the 8-oxoG(-H7)⁺  : C deprotonation from all possible active sites is infeasible, indicating the inaccessible second proton loss and the lack of essential intermediate 2-amino-7,9-dihydropurine-6,8-dione (8-oxoG^OX ). This makes 8-oxoG(-H7)⁺ act as the precursor of hydration leading to the generation of protonated 5-HO-8-oxoG by stepwise fashion in base pair, which would initiate the step down guanidinohydantoin (Gh) pathway. These results clearly specify the structure-dependent transformation for 8-oxoG⋅⁺ and verify the emergence of protonated 5-HO-8-oxoG in base pair.

Measurement of Enthalpies and Entropies of Activation as a Function of Pairwise Distance for the Pairwise Relative Diffusion of SrI2 in Water over Lengthscales from 6 Å to 40 Å

Quasi-elastic neutron scattering (QENS) has been used to provide insight into the motions within solutions for many decades, and coherent QENS (CQENS) determines the motions of one ion relative to...

Supercritical Water is not Hydrogen Bonded

Thinking about water is inextricably linked to hydrogen bonds, which are highly directional in character and determine the unique structure of water, in particular its tetrahedral H-bond network. Here, we assess if this common connotation also holds for supercritical water. We employ extensive ab initio molecular dynamics simulations to systematically monitor the evolution of the H-bond network mode of water from room temperature, where it is the hallmark of its fluctuating three-dimensional network structure, to supercritical conditions. Our simulations reveal that the oscillation period required for H-bond vibrations to occur exceeds the lifetime of H-bonds in supercritical water by far. Instead, the corresponding low-frequency intermolecular vibrations of water pairs as seen in supercritical water are found to be well represented by isotropic van-der-Waals interactions only. Based on these findings, we conclude that water in its supercritical phase is not a H-bonded fluid.

Deprotonation of Guanine Radical Cation G•+ Mediated by the Protonated Water Cluster

Proton transfer is regarded as a fundamental process in chemical reactions of DNA molecules and continues to be an active research theme due to the connection with charge transport and oxidation damage of DNA. For the guanine radical cation (G^•+) derived from one-electron oxidation, experiments suggest a facile proton transfer within the G^•+:C base pair, and a rapid deprotonation from N1 in free base or single-strand DNA. To address the deprotonation mechanism, we perform a thorough investigation on deprotonation of G^•+ in free G base by combining density functional theory (DFT) and laser flash photolysis spectroscopy. Experimentally, kinetics of deprotonation is monitored at temperatures varying from 280 to 298 K, from which the activation energy of 15.1 ± 1.5 kJ/mol is determined for the first time. Theoretically, four solvation models incorporating explicit waters and the polarized continuum model (PCM), i.e., 3H₂O-PCM, 4H₂O-PCM, 5H₂O-PCM, and 7H₂O-PCM models are used to calculate deprotonation potential energy profile, and the barriers of 5.5, 13.4, 14.4, and 13.7 kJ/mol are obtained, respectively. It is shown that at least four explicit waters are required for properly simulating the deprotonation reaction, where the participation of protonated water cluster plays key roles in facilitating the proton release from G^•+.

Assessing the properties of supercritical water in terms of structural dynamics and electronic polarization effects

Evolution of water's structural dynamics from ambient liquid to supercritical dense liquid-like and dilute gas-like conditions.

Nanoscale Mobility of Aqueous Polyacrylic Acid in Dental Restorative Cements

Hydrogen dynamics in a time range from hundreds of femtoseconds to nanoseconds can be directly analyzed using neutron spectroscopy, where information on the inelastic and quasi-elastic scattering, hereafter INS and QENS, can be obtained. In this study, we applied these techniques to understand how the nanoscale mobility of the aqueous solution of polyacrylic acid (PAA) used in conventional glass ionomer cements (GICs) changes under confinement. Combining the spectroscopic analysis with calorimetric results, we were able to separate distinct motions within both the liquid and the GICs. The QENS analysis revealed that the self-diffusion translational motion identified in the liquid is also visible in the GIC. However, as a result of the formation of the cement matrix and its setting, both translational diffusion and residence time differed from the PAA solution. When comparing the local diffusion obtained for the selected GIC, the only noticeable difference was observed for the slow dynamics associated with the polymer chain. Additionally, over short-term aging, progressive water binding to the polymer chain occurred in one of the investigated GICs. Finally, a considerable change in the density of the GIC without progressive water binding indicates an increased polymer cross-linking. Taken together, our results suggest that accurate and deep understanding of polymer-water binding, polymer cross-linking, as well as material density changes occurring during the maturation process of GIC are necessary for the development of advanced dental restorative materials.

The relative diffusive transport rate of SrI2 in water changes over the nanometer length scale as measured by coherent quasielastic neutron scattering

X-ray and neutron scattering have been used to provide insight into the structures of ionic solutions for over a century, but the probes have covered distances shorter than 8 Å. For the non-hydrolyzing salt SrI2 in aqueous solution, a locally ordered lattice of ions exists that scatters slow neutrons coherently down to at least 0.1 mol L(-1) concentration, where the measured average distance between scatterers is over 18 Å. To investigate the motions of these scatterers, coherent quasielastic neutron scattering (CQENS) data on D2O solutions with SrI2 at 1, 0.8, 0.6, and 0.4 mol L(-1) concentrations was obtained to provide an experimental measure of the diffusive transport rate for the motion between pairs of ions relative to each other. Because CQENS measures the motion of one ion relative to another, the frame of reference is centered on an ion, which is unique among all diffusion measurement methods. We call the measured quantity the pairwise diffusive transport rate Dp. In addition to this ion centered frame of reference, the diffusive transport rate can be measured as a function of the momentum transfer q, where q = (4π/λ)sin θ with a scattering angle of 2θ. Since q is related to the interion distance (d = 2π/q), for the experimental range 0.2 Å(-1)≤q≤ 1.0 Å(-1), Dp is, then, measured over interion distances from 40 Å to ≈6 Å. We find the measured diffusional transport rates increase with increasing distance between scatterers over the entire range covered and interpret this behavior to be caused by dynamic coupling among the ions. Within the model of Fickian diffusion, at the longer interionic distances Dp is greater than the Nernst-Hartley value for an infinitely dilute solution. For these nm-distance diffusional transport rates to conform with the lower, macroscopically measured diffusion coefficients, we propose that local, coordinated counter motion of at least pairs of ions is part of the transport process.

Ultrafast Energy Transfer from Solvent to Solute Induced by Subpicosecond Highly Intense THz Pulses

The ultrafast energy transfer from an intense, subpicosecond THz pulse to bulk water at 300 K and density 1 g/cm(3) is simulated by ab initio molecular dynamics with explicit inclusion of the laser pulse. A 200 fs subcycle pulse of intensity 5 × 10(12) W/cm(2) corresponding to a peak field amplitude of 0.6 V/Å and achievable nowadays using optical rectification techniques results in a temperature jump from 300 K up to ∼1000 K within the first picosecond after the pulse. We discuss in detail the time-dependent structural changes caused by the THz pulse in the water medium and suggest possible ways to measure those changes by pump-probe experimental techniques. The ultrafast energy transfer from the energized water molecules to a solute molecule is studied on a test system, phenol. We find that phenol is, in the gas phase, insensitive to the THz pulse and only gains energy in solution via collisional energy transfer with the water molecules in its environment. The reason for this is found in the mode of interaction of the THz pulse with the aqueous medium. In short, water molecules respond mainly through their permanent dipole moments trying to orient themselves in the strong electric field of the pulse and disrupting their hydrogen-bonding structure. As compared with the water molecule, phenol has a smaller but still substantial permanent dipole moment. The moments of inertia of phenol are, however, too large for it to rotate in the short duration of the THz pulse. Therefore, the direct heating-up mechanism is mostly selective to the solvent molecules, whereas the solute heats up indirectly via collisions with its hot environment in about 1 to 2 ps.

Small-angle scattering and the structure of ambient liquid water

Structural polyamorphism has been promoted as a means for understanding the anomalous thermodynamics and dynamics of water in the experimentally inaccessible supercooled region. In the metastable liquid region, theory has hypothesized the existence of a liquid-liquid critical point from which a dividing line separates two water species of high and low density. A recent small-angle X-ray scattering study has claimed that the two structural species postulated in the supercooled state are seen to exist in bulk water at ambient conditions. We analyze new small-angle X-ray scattering data on ambient liquid water taken at third generation synchrotron sources, and large 32,000 water molecule simulations using the TIP4P-Ew model of water, to show that the small-angle region measures standard number density fluctuations consistent with water's isothermal compressibility temperature trends. Our study shows that there is no support or need for heterogeneities in water structure at room temperature to explain the small-angle scattering data, as it is consistent with a unimodal density of the tetrahedral liquid at ambient conditions.

Dynamics in Clays - Combining Neutron Scattering and Microscopic Simulation

Mobility of ions and water in clays is at the heart of their remarkable properties of water retention and ion-exchange. It has been addressed here using two microscopic techniques: neutron scattering and molecular dynamics simulations. Neutron scattering gives access exclusively to water dynamics in clays, due to the exceptional sensitivity of neutrons to H atoms. The data interpretation can be challenging, especially for natural clays such as montmorillonite, with inhomogeneous swelling characteristics. A great improvement is achieved with the use of synthetic materials, as demonstrated here on the case of synthetic (fluoro)hectorite. The standard analytical models for long-range diffusive motion, isotropic translation and its derivative, powder averaged two dimensional translation, have been used to interpret the neutron scattering data. They both agree on the order of magnitude for the diffusion coefficient of water in monohydrated and bihydrated clays, 10−10 m2s−1 and 10−9 m2s−1 respectively. While the two-dimensional nature of water diffusion in clays is seen clearly from molecular dynamics simulations, its signature in neutron scattering data is obscured by the powder-averaging of the signal. A novel method, based on a multi-resolution analysis of scattering functions from powder samples, allows never-the-less a clear determination of the dimensionality of water motion in the system. Extracting information on local water motion is difficult on the basis of neutron scattering data only. Various models for localised motion, rotation on a sphere or jump diffusion, have been proposed and used to interpret the observed neutron data, however their applicability is questionable in light of information from molecular dynamics simulations. Aside from aiding the interpretation of neutron scattering data, MD simulations are most valuable in providing information on the behaviour of ions in clays. MD estimates the interlayer ion coefficients as of the some order of magnitude as water, even if the details of ionic motion are strikingly different between the two ions considered here, Na+ and Cs+. Further, MD has also allowed to address the topic of ion exchange between clay interlayers and bulk aqueous solution. The microscopic picture of water and ion motion in clays, emerging from neutron scattering and MD simulations, should be treated as a building block of the overall modelling of macroscopic transport in clays, the ultimate property of interest for many clay applications.

Water Dynamics in Hardened Ordinary Portland Cement Paste or Concrete: From Quasielastic Neutron Scattering

Portland cement reacts with water to form an amorphous paste through a chemical reaction called hydration. In concrete the formation of pastes causes the mix to harden and gain strength to form a rock-like mass. Within this process lies the key to a remarkable peculiarity of concrete: it is plastic and soft when newly mixed, strong and durable when hardened. These qualities explain why one material, concrete, can build skyscrapers, bridges, sidewalks and superhighways, houses, and dams. The character of the concrete is determined by the quality of the paste. Creep and shrinkage of concrete specimens occur during the loss and gain of water from cement paste. To better understand the role of water in mature concrete, a series of quasielastic neutron scattering (QENS) experiments were carried out on cement pastes with water/cement ratio varying between 0.32 and 0.6. The samples were cured for about 28 days in sealed containers so that the initial water content would not change. These experiments were carried out with an actual sample of Portland cement rather than with the components of cement studied by other workers. The QENS spectra differentiated between three different water interactions: water that was chemically bound into the cement paste, the physically bound or "glassy water" that interacted with the surface of the gel pores in the paste, and unbound water molecules that are confined within the larger capillary pores of cement paste. The dynamics of the "glassy" and "unboud" water in an extended time scale, from a hundred picoseconds to a few nanoseconds, could be clearly differentiated from the data. While the observed motions on the picosecond time scale are mainly stochastic reorientations of the water molecules, the dynamics observed on the nanosecond range can be attributed to long-range diffusion. Diffusive motion was characterized by diffusion constants in the range of (0.6-2) 10(-9) m(2)/s, with significant reduction compared to the rate of diffusion for bulk water. This reduction of the water diffusion is discussed in terms of the interaction of the water with the calcium silicate gel and the ions present in the pore water.

Molecular view of water dynamics near model peptides

Incoherent quasi-elastic neutron scattering (QENS) has been used to measure the dynamics of water molecules in solutions of a model protein backbone, N-acetyl-glycine-methylamide (NAGMA), as a function of concentration, for comparison with results for water dynamics in aqueous solutions of the N-acetyl-leucine-methylamide (NALMA) hydrophobic peptide at comparable concentrations. From the analysis of the elastic incoherent structure factor, we find significant fractions of elastic intensity at high and low concentrations for both solutes, which corresponds to a greater population of protons with rotational time scales outside the experimental resolution (>13 ps). The higher-concentration solutions show a component of the elastic fraction that we propose is due to water motions that are strongly coupled to the solute motions, while for low-concentration solutions an additional component is activated due to dynamic coupling between inner and outer hydration layers. An important difference between the solute types at the highest concentration studied is found from stretched exponential fits to their experimental intermediate scattering functions, showing more pronounced anomalous diffusion signatures for NALMA, including a smaller stretched exponent beta and a longer structural relaxation time tau than those found for NAGMA. The more normal water diffusion exhibited near the hydrophilic NAGMA provides experimental support for an explanation of the origin of the anomalous diffusion behavior of NALMA as arising from frustrated interactions between water molecules when a chemical interface is formed upon addition of a hydrophobic side chain, inducing spatial heterogeneity in the hydration dynamics in the two types of regions of the NALMA peptide. We place our QENS measurements on model biological solutes in the context of other spectroscopic techniques and provide both confirming as well as complementary dynamic information that attempts to give a unifying molecular view of hydration dynamics signatures near peptides and proteins.

Status of experiments probing the dynamics of water in confinement

In many relevant situations, water is not in its bulk form but is instead attached to some substrates or filling some cavities. We shall call water in the latter environment "confined or interfacial water" as opposed to bulk water. This confined water is essential for the stability and function of biological macromolecules. In this review paper, we present the more recent up to date account of the dynamics of confined water as compared with that of bulk water. Various techniques are used to study the dynamics of confined water. Among them, quasi-elastic and inelastic neutron scattering is a powerful tool to study translational and rotational diffusion as well as vibrational density of states of confined water. Various examples involving water confined in porous media, adsorbed on surface of ionic crystals, in the presence of organic solutes and at the surface of biological molecules are presented. The combined effects of the hydration level and the temperature on the retardation of the water molecules motions are discussed on the basis of phenomenological models as well as of power law fits based on the Mode Coupling Theory.