Molecular dynamics study of the hydration of the hydroxyl radical at body temperature

Classical molecular dynamics (MD) simulation of ˙OH in liquid water at 37 °C has been performed using flexible models of the solute and solvent molecules. We derived the Morse function describing the bond stretching of the radical and the potential for ˙OH-H(2)O interactions, including short-range interactions of hydrogen atoms. Scans of the potential energy surface of the ˙OH-H(2)O complex have been performed using the DFT method with the B3LYP functional and the 6-311G(d,p) basis set. The DFT-derived partial charges, ±0.375e, and the equilibrium bond-length, 0.975 ?, of ˙OH resulted in the dipole moment of 1.76 D. The radical-water radial distribution functions revealed that ˙OH is not built into the solvent structure but it rather occupies distortions or cavities in the hydrogen-bonded network. The solvent structure at 37 °C has been found to be the same as that of pure water. The hydration cage of the radical comprises 13-14 water molecules. The estimated hydration enthalpy -42 ± 5 kJ mol(-1) is comparable with the experimental value -39 ± 6 kJ mol(-1) for 25 °C. Inspection of hydrogen bonds showed the importance of short-range interaction of hydrogen atoms and indicated that neglect of the angular condition greatly overestimates the number of the H-acceptor radical-water bonds. The mean number ?n = 0.85 of radical-water H-bonds has been calculated using geometric definition of H-bond and ?n = 0.62 has been obtained when the energetic condition, E(da)≤-8 kJ mol(-1), was additionally considered. The continuous lifetimes of 0.033 ps and 0.024 ps have been estimated for the radical H-donor and the H-acceptor bonds, respectively. Within statistical uncertainty the radical self-diffusion coefficient, (2.9 ± 0.6) × 10(-9) m(2) s(-1), is the same as (3.1 ± 0.5) × 10(-9) m(2) s(-1) calculated for water in solution and in pure solvent. To the best of our knowledge, this is the first study of the ˙OH(aq) properties at a biologically relevant body temperature.     

Classical molecular-dynamics simulation of the hydroxyl radical in water

We have studied the hydration and diffusion of the hydroxyl radical OH0 in water using classical molecular dynamics. We report the atomic radial distribution functions, hydrogen-bond distributions, angular distribution functions, and lifetimes of the hydration structures. The most frequent hydration structure in the OH0 has one water molecule bound to the OH0 oxygen (57% of the time), and one water molecule bound to the OH0 hydrogen (88% of the time). In the hydrogen bonds between the OH0 and the water that surrounds it the OH0 acts mainly as proton donor. These hydrogen bonds take place in a low percentage, indicating little adaptability of the molecule to the structure of the solvent. All hydration structures of the OH0 have shorter lifetimes than those corresponding to the hydration structures of the water molecule. The value of the diffusion coefficient of the OH0 obtained from the simulation was 7.1x10(-9) m2 s(-1), which is higher than those of the water and the OH-.     

Hydroxidmonohydrate des Kaliums und Rubidiums; Verbindungen,deren Atomanordnungen die Schreibweise K(H2O)OH bzw. Rb(H2O)OH nahelegen

Hydroxide Monohydrates of Potassium and Rubidium; Compounds with Atomic Arrangements which Suggest the Formula K(H₂O)OH and Rb(H₂O)OH Single crystals for x-ray structure investigations of the monohydrates of potassium and rubidium hydroxides were obtained by recrystallization of microcrystalline sampels in supercritical ammonia as solvent. The structure determination on both structurally closely related compounds was successful up to the localization of the hydrogen positions. Besides the monohydrates were characterized by IR spectra and thermochemical data. The atomic arrangement of the compounds is discussed in comparison to the one of substances as PbFCl, γ-AlOOH etc. In addition to the chemical bonds in the stated compounds both monohydrates show one-dimensional infinite hydrogen bridges between the H atoms of the water molecules and the hydroxide ions; furthermore weak H bonds connect the OH^? ions. Because the hydroxide ions are involved in two bridge-bindung systems water molecules are the nearest neigh-bours of the cations.     

A theoretical study on anomalous temperature dependence of pKw of water

pH, with its well-known value of 7 at ambient condition, is a most basic property of water, with wide implications in chemistry and biology. The pH value is determined by the tendency of autoionization of water molecules into ion pairs, H(+) and OH(-), and is expected to vary extensively with the water condition, which determines the stability of the ion pairs. When temperature rises from the normal to the supercritical region, the pH of water experimentally exhibits complex, nonmonotonic temperature dependence, that is, it first decreases from 7 and then increases rapidly. Accurate theoretical evaluation of pH and microscopic understanding of this anomalous behavior have proven to be a challenging task because the hydration of these ions, especially for OH(-), is very difficult to reproduce. In the present study a molecular simulation is performed to understand this peculiar temperature dependence. The imbalance between the ion-water and the water-water molecular interaction strengths and the concomitant water density enhancement in the hydration shell, observed in the supercritical liquids, serve to put a subtle balance to produce this temperature dependence of the pH value. It is found that the large charge transfers from H(+) and OH(-) to the surrounding water molecules take place. In these transfers, not only water molecules in the neighboring hydration shell but also those in the outer hydration shell play a significant role. The coordination number of water molecules around OH(-) is found to be 4.5 at 300 K, which decreases slowly with temperature, for example, 4 at 800 K, in the present calculation.     

An application of the novel quantum mechanical/molecular mechanical method combined with the theory of energy representation: An ionic dissociation of a water molecule in the supercritical water

A novel quantum chemical approach recently developed has been applied to an ionic dissociation of a water molecule (2H(2)O-->H(3)O(+)+OH(-)) in ambient and supercritical water. The method is based on the quantum mechanical/molecular mechanical (QM/MM) simulations combined with the theory of energy representation (QM/MM-ER), where the energy distribution function of MM solvent molecules around a QM solute serves as a fundamental variable to determine the hydration free energy of the solute according to the rigorous framework of the theory of energy representation. The density dependence of the dissociation free energy in the supercritical water has been investigated for the density range from 0.1 to 0.6 g/cm(3) with the temperature fixed at a constant. It has been found that the product ionic species significantly stabilizes in the high density region as compared with the low density. Consequently, the dissociation free energy decreases monotonically as the density increases. The decomposition of the hydration free energy has revealed that the entropic term (-TDeltaS) strongly depends on the density of the solution and dominates the behavior of the dissociation free energy with respect to the variation of the density. The increase in the entropic term in the low density region can be attributed to the decrease in the translational degrees of freedom brought about by the aggregation of solvent water molecules around the ionic solute.     

Transition from patchlike to clusterlike inhomogeneity arising from hydrogen bonding in water

Assembling of water molecules via hydrogen bonding has been studied by molecular dynamics simulations using flexible potential model. The relationship between the number of H-bonds per molecule, n(HB), the size of H-bonded nets, k, and the size of patches of four-bonded molecules, k(4), has been examined for several thermodynamic states of water ranging from ambient to supercritical conditions. Two kinds of structural inhomogeneity have been found: the patchlike associated with the mean n(HB)> 2.0 and the clusterlike for n(HB)< 1.9. In compressed water up to ~473 K patches coexist with less ordered nets, both constituting the gel-like H-bonded network. The size of patches steeply decreases with the increasing temperature and the decreasing density of water. The inhomogeneity resulting from the presence of patches disappears above 473 K. This feature is associated with the rapid increase in the fraction of unbound molecules and with the breakage of the gel-like network into a variety of H-bonded clusters leading to the clusterlike structural inhomogeneity. In contrast to the patchlike inhomogeneity an increase in temperature and a decrease in density make this kind of inhomogeneity more pronounced. A degree of connectivity of H-bonds has been characterized by a parameter P(g) defined as the total fraction of molecules belonging to the H-bonded clusters of size k ≥ 5. The simulation-derived values of P(g) agree well with the predictions of the random bond theory giving the explicit expression for P(g) as a function of the mean n(HB). Going from ambient to supercritical conditions, we have found that the patchlike inhomogeneity is connected with the very slight reduction in P(g), whereas the clusterlike inhomogeneity generates a steep linear decrease of P(g) with the decreasing mean n(HB). The self-diffusion coefficient calculated for the thermodynamic states of water showing the clusterlike inhomogeneity has occurred to be inversely proportional to the density. We have also found that the clusterlike inhomogeneity is associated with the linear correlation between P(g) and the macroscopic properties of water: the static dielectric constant, the viscosity, and the density. The provided relationships allow one to estimate the degree of connectivity of hydrogen bonds from the measured macroscopic quantities.     

Novel quantum mechanical/molecular mechanical method combined with the theory of energy representation: free energy calculation for the Beckmann rearrangement promoted by proton transfers in the supercritical water

The Beckmann rearrangement of acetone oxime promoted by proton transfers in the supercritical water has been investigated by means of the hybrid quantum mechanical/molecular mechanical approach combined with the theory of energy representation (QM/MM-ER) recently developed. The transition state (TS) structures have been explored by ab initio calculations for the reaction of hydrated acetone oxime on the assumption that the reaction is catalyzed by proton transfers along the hydrogen bonds connecting the solute and the solvent water molecules. Up to two water molecules have been considered as reactants that take part in the proton transfers. As a result of the density functional theory calculations with B3LYP functional and aug-cc-pVDZ basis set, it has been found that participation of two water molecules in the reaction reduces the activation free energy by -12.3 kcal/mol. Furthermore, the QM/MM-ER simulations have revealed that the TS is more stabilized than the reactant state in the supercritical water by 2.7 kcal/mol when two water molecules are involved in the reaction. Solvation free energies of the reactant and the TS have been decomposed into terms due to the electronic polarization of the solute, electron density fluctuation, and others to elucidate the origin of the stabilization of the TS as compared with the reactant. It has been revealed that the promotion of the chemical reaction due to the hydration mainly originates from the interaction between the nonpolarized solute and the solvent water molecules at the supercritical state.     

Hydroxyl radical and hydroxide ion in liquid water: a comparative electron density functional theory study

Ab initio density functional theory molecular dynamics simulations of the solvated states of the hydroxyl radical and hydroxide ion are performed using the Becke-Lee-Yang-Parr (BLYP) exchange-correlation functional (Becke, A. D. Phys. Rev. A 1988, 38, 3098. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785). The structures of the solvation shells of the two species are examined. It is found that the OH radical forms a relatively well-defined solvation complex with four neighboring water molecules. Three of these molecules are hydrogen bonded to the OH, while the fourth is hemibonded via a three-electron two-centered bond between the oxygen atoms of the OH and water. The activity and the diffusion mechanism of the OH radical in water is discussed in comparison with the OH- ion. Although the results are partially influenced by the tendency of the BLYP density functional to overestimate hemibonded structure, the present simulations suggest that the widely accepted picture of rapid diffusion of OH radical in water through hydrogen exchange reaction may need to be reconsidered.     

Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites,solvent density,and solvent dipole

The hydration structure of human lysozyme was studied with cryogenic X-ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 A provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1-ns simulation trajectories: the solvent density reflecting the time-averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long-distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration.     

Effect of water density on methanol oxidation kinetics in supercritical water

We oxidized methanol in supercritical water at 500 degrees C to explore the influence of the water concentration (or density) on the kinetics. The rate increased as the water concentration increased from 1.8 to 5.7 mol/L. This effect of water density on the kinetics observed experimentally was quantitatively reproduced by a previously validated mechanism-based, detailed chemical kinetics model. In this model, reactions of OH radicals with methanol were the fastest methanol removal steps. The rates of these removal steps increased with water density at 500 degrees C because the OH radical concentration increased. The OH radical concentration increased with density because the rates of the steps H + H2O = OH + H2 and CH3 + H2O = OH + CH4, which produce OH radicals, increased. Thus, the main role of water in accelerating methanol oxidation kinetics at 500 degrees C is as a hydrogen donor to a radical (R) in steps such as R + H2O = OH + RH. This system provides a striking example of SCW being involved on the molecular level in the free-radical oxidation as a reactant in elementary steps.     

High-density hydration layer of lysozymes: molecular dynamics decomposition of solution scattering data

A characterization of the physical properties of protein hydration water is critical for understanding protein structure and function. Recent small-angle X-ray and neutron scattering data indicate that the density of water on the surface of lysozyme is significantly higher than in bulk water. Here, we provide an interpretation of the scattering results using a molecular dynamics simulation, which allows us to make quantitative predictions about density variations in the first hydration shell. The perturbation relative to bulk water involves statistically significant changes in the average water structure in the first hydration layer. The water density in the first hydration shell is increased by 5% with respect to the bulk. In regions of higher water density, the water dipoles align more parallel to each other and the number of hydrogen bonds per water molecule is higher. Increased water density is found for water molecules interacting with hydrogen and carbon atoms in the backbone or with nonpolar or negatively charged side-chain groups.     

Acetone hydration in supercritical water: (13)C-NMR spectroscopy and Monte Carlo simulation

The (13)C-NMR chemical shift of acetone delta((13)C[Double Bond]O) was measured in aqueous solution at high temperatures up to 400 degrees C and water densities of 0.10-0.60 g/cm(3) for the study of hydration structure in the supercritical conditions. The average number N(HB) of hydrogen bonds (HBs) between an acetone and solvent waters and the energy change DeltaE upon the HB formation were evaluated from the delta and its temperature dependence, respectively. At 400 degrees C, N(HB) is an increasing function of the water density, the increase being slower at higher water densities. The acetone-water HB formation is exothermic in supercritical water with larger negative DeltaE at lower water densities (-3.3 kcal/mol at 0.10 g/cm(3) and -0.3 kcal/mol at 0.60 g/cm(3)), in contrast to the positive DeltaE in ambient water (+0.078 kcal/mol at 4 degrees C). The corresponding Monte Carlo simulations were performed to calculate the radial and orientational distribution functions of waters around the acetone molecule. The density dependence of N(HB) calculated at 400 degrees C is in a qualitative agreement with the experimental results. In the supercritical conditions, the HB angle in a neighboring acetone-water pair is weakly influenced by the water density, because of the absence of collective HB structure. This is in sharp contrast to the hydration structure in ambient water, where the acetone-water HB formation is orientationally disturbed by the tetrahedral HB network formation among the surrounding waters.     

Hydroxyl radical in aqueous solution: Computer simulation

Molecular dynamics simulations of hydroxyl radical in water are carried out by use of a classical simple point charge extended (SPC/E) water model and a similar point charge model for hydroxyl radical. Structural and dynamical properties are studied along the coexistence curve of SPC/E water at 298, 373, 473, 573, and 633 K and above its critical point at 683, 733, 783, and 833 K with density fixed at 0.3 g/cm3. Dramatic changes in the diffusion dynamics of water and hydroxyl radical near the critical point are related to the reorganization of the three-dimensional structure of water around hydroxyl radical, as revealed by the study of the spatial distribution functions. This study helps us understand the kinetics of oxidation reactions in high-temperature water.     

Dimerisation of urea in water solution: a quantum mechanical investigation

The effect of water solvation on the structure and stability of cyclic dimers of urea has been investigated with the aid of density functional theory at the B3LYP/6-311++G** level. Several hydration models have been discussed. Specific solvent effects have been simulated through single and multiple water-urea interactions involving all the hydration sites of urea. The bulk solvent effects have been estimated through polarised continuum models. Under all the hydration patterns cyclic dimers continue to be stable structures although the solvent weakens the urea-urea interaction. Single and multiple specific urea-water interactions are competitive with urea dimerisation. The anticooperative nature of the two intermolecular interactions is largely due to the changes on sigma- and pi-electron density of urea caused by hydrogen bonding with water. The stability of the dimer is however, lost within a few ps when the hydrated dimer is described by a quantum mechanical molecular dynamics approach (ADMP). The cyclic dimer evolves towards structures where urea molecules are linked not more directly but through water molecules which have a bridge function.     

The role of local structure on formic acid decomposition in supercritical water: A hybrid quantum mechanics/Monte Carlo study

We explored water-assisted decompositions of formic acid in supercritical water in terms of local structure near reactant. A hybrid quantum mechanics/molecular mechanics (QM/MM) simulation used in this paper includes QM part as first solvation shell members around the reactant. A present QM/MM approach can simulate supercritical water solution with a reasonable computational load while keeping the simulation preciseness because a density functional theory of B3LYP/6-31+G(d) level was iterated at every 1000 Monte Carlo solute moves. The formic acid converts mainly decarboxylation by water-assisted mechanism, and the coordinated water molecules play an important role for understanding supercritical water density dependence of the reaction. We analyzed a contour map based on the solute–solvent interaction energy along with the reaction pathway. Coordinated water molecule restricted the dehydration pathway by means of hydrogen bond with formic acid, however, the coordinated water promotes the decarboxylation pathway by means of stabilization of the transition state structure with one catalytic water molecule. The contour map of the pair interaction energy along the reaction path elucidates the role of local structure on reactions in supercritical water.     

Structure and hydration of L-proline in aqueous solutions

The structure and hydration of L-proline in aqueous solution have been investigated using a combination of neutron diffraction with isotopic substitution, empirical potential structure refinement modeling, and small-angle neutron scattering at three concentrations, 1:10, 1:15, and 1:20 proline/water mole ratios. In each solution the carboxylate oxygen atoms from proline accept less than two hydrogen bonds from the surrounding water solvent and the amine hydrogen atoms donate less than one hydrogen bond to the surrounding water molecules. The solute-solute radial distribution functions indicate relatively weak interactions between proline molecules, and significant clustering or aggregation of proline is absent at all these concentrations. The spatial density distributions for the hydration of the COO- group in proline show a similar shape to that found previously in L-glutamic acid in aqueous solution but with a reduced coordination number.     

Hydration of sodium, potassium, and chloride ions in solution and the concept of structure maker/breaker

Neutron diffraction data with hydrogen isotope substitution on aqueous solutions of NaCl and KCl at concentrations ranging from high dilution to near-saturation are analyzed using the Empirical Potential Structure Refinement technique. Information on both the ion hydration shells and the microscopic structure of the solvent is extracted. Apart from obvious effects due to the different radii of the three ions investigated, it is found that water molecules in the hydration shell of K+ are orientationally more disordered than those hydrating a Na+ ion and are inclined to orient their dipole moments tangentially to the hydration sphere. Cl- ions form instead hydrogen-bonded bridges with water molecules and are readily accommodated into the H-bond network of water. The results are used to show that concepts such as structure maker/breaker, largely based on thermodynamic data, are not helpful in understanding how these ions interact with water at the molecular level.     

Density dependence of hydrogen bonding and the translational-orientational structural order in supercritical water: a molecular dynamics study

Molecular dynamics simulation have been performed with a wide range of densities along a near critical isotherm of supercritical water (SCW) in order to study the density dependence of the structure order and hydrogen bonding (HB). It is revealed that the translational structure order is nearly invariant while the orientational tetrahedral structure order is very sensitive to the bulk density under supercritical conditions. Meanwhile, some energetically unfavorable intermediate water dimer structures are found to appear under supercritical conditions due to the reduced energy difference and the enhanced energy fluctuation. As a consequence, a general geometrical criterion or the inclusion of a energy-based criterion instead of currently widely adopted pure r(OH)-based geometric criterion is suggested to be used in the HB statistics under supercritical conditions. It is found that the average HB number per H(2)O molecule (n(HB)) reduces with the decreasing SCW bulk density although a given pair of H(2)O molecules are shown to have a stronger ability to form a hydrogen bond under lower SCW bulk densities. Accordingly, the orientational tetrahedral structure order q decreases with the reducing bulk density under supercritical conditions. However, when the fluid is dilute with ρ ≤ 0.19ρ(c) (ρ(c) = 0.322 g/cm(3)), the energy fluctuation increases sharply and the short-range order is destroyed, signifying the supercritical fluid (SCF)-gas state transition. Accordingly, the orientational tetrahedral structure order q gets reversal around ρ = 0.19ρ(c) and approaches zero under very dilute conditions. The sensitivity of the orientational order to the density implies the microscopic origin of the significant dependence of SCF's physicochemical properties on the pressure.     

Structural and electronic evolution of the As(OH)3 molecule in high temperature aqueous solutions: an x-ray absorption investigation

The geometrical and electronic structure of the arsenious acid molecule As(OH)(3) in aqueous solutions has been investigated by x-ray absorption spectroscopy (XAS) within extended x-ray absorption spectroscopy (EXAFS) and x-ray absorption near edge structure (XANES), using realistic first-principle calculations in the latter case. This investigation was performed on aqueous solutions of arsenious acid from ambient to supercritical conditions (P = 250 and 600 bars, T 相似文献   

Mechanism for degradation of Nafion in PEM fuel cells from quantum mechanics calculations

We report results of quantum mechanics (QM) mechanistic studies of Nafion membrane degradation in a polymer electrolyte membrane (PEM) fuel cell. Experiments suggest that Nafion degradation is caused by generation of trace radical species (such as OH(●), H(●)) only when in the presence of H(2), O(2), and Pt. We use density functional theory (DFT) to construct the potential energy surfaces for various plausible reactions involving intermediates that might be formed when Nafion is exposed to H(2) (or H(+)) and O(2) in the presence of the Pt catalyst. We find a barrier of 0.53 eV for OH radical formation from HOOH chemisorbed on Pt(111) and of 0.76 eV from chemisorbed OOH(ad), suggesting that OH might be present during the ORR, particularly when the fuel cell is turned on and off. Based on the QM, we propose two chemical mechanisms for OH radical attack on the Nafion polymer: (1) OH attack on the S-C bond to form H(2)SO(4) plus a carbon radical (barrier: 0.96 eV) followed by decomposition of the carbon radical to form an epoxide (barrier: 1.40 eV). (2) OH attack on H(2) crossover gas to form hydrogen radical (barrier: 0.04 eV), which subsequently attacks a C-F bond to form HF plus carbon radicals (barrier as low as 1.00 eV). This carbon radical can then decompose to form a ketone plus a carbon radical with a barrier of 0.86 eV. The products (HF, OCF(2), SCF(2)) of these proposed mechanisms have all been observed by F NMR in the fuel cell exit gases along with the decrease in pH expected from our mechanism.