Residence Time Of Water Molecules Research Articles

Residence times of water molecules on stainless steel and aluminum surfaces in vacuum and atmosphere

The adsorption and desorption phenomena of water molecules on stainless steel and aluminum surfaces have been studied by means of tritium tracer technique (TTT) with special emphasis on potential differences in the residence times in atmosphere and vacuum. Samples with a geometrical surface area of about 2cm2 have been exposed in an atmospheric environment loaded with a vapor pressure of HTO (tritium-labeled water) of known specific activity, and the adsorbed amount of water has been determined by liquid-scintillation counting technique. In previous studies it was found that, in atmosphere, adsorbed water quantities and their reproducibility depend significantly on the cleanliness of the surfaces. Furthermore, it was observed that desorption into atmosphere (or exchange with atmospheric humidity) is a rather slow process with a few percent of the adsorbed water molecules staying even for several days and with the water coverage versus time t characterized approximately by a 1∕tα law with α≈0.4. In this work, TTT measurements of water desorption have been extended into high vacuum. HTO-covered specimens have been transferred into a vacuum chamber soon after HTO exposure and have been kept under high vacuum for a certain vacuum desorption time which was varied from minutes to several days. It was found that water desorption from stainless steel and aluminum surfaces in vacuum is slower than in atmosphere with the residual coverage again described approximately by a 1∕tα law but now with α≈0.14 (stainless steel) and α≈0.17 (Al). Water desorption rates calculated from coverage versus time are within the range of outgassing data reported in literature, indicating that the TTT method can be a powerful tool for the characterization of potential new vacuum materials even if just small specimens are available.

Development of New Cd2+ and Pb2+ Lennard-Jones Parameters for Liquid Simulations

We present new Lennard-Jones parameters for Cd2+ and Pb2+ ion-water interactions and describe a general methodology to obtain these parameters for any ion. Our strategy is based on the adjustment of ion parameters to reproduce simultaneously experimental absolute hydration free energy and structural properties, namely, g(r) and coordination numbers, obtained from X-ray liquid scattering and quantum mechanical/molecular mechanical (QM/MM) calculations. The validation of the obtained parameters is made by the calculation of dynamical properties and comparing them with experimental values and theoretical results from the literature. The transferability of parameters is checked by the calculation of thermodynamic, structural, and dynamical properties cited above with four different water models. The results obtained for Cd2+ and Pb2+ show an overall agreement with reference values. The absolute hydration free energy calculated with the TIP3P, SPC/E, SPC, and TIP4P water models presents, respectively, percent differences of 3.8, 3.0, 4.3, and 7.2% for lead(II) and 9.8, 8.4, 10.2, and 14.1% for cadmium(II) when compared with experimental values. Ion-water mean distance and coordination numbers for the first coordination shell are in good agreement with experimental and QM/MM results for both ions. Cd2+ shows a lesser diffusion coefficient compared to that of Pb2+ despite its smaller atomic radius, indicating a more persistent first coordination shell for the cadmium(II) ion, a result confirmed with calculations of the mean residence time of water molecules in the first coordination shell.

A Combined QM/MM Molecular Dynamics Simulations Study of Nitrate Anion (NO3‐) in Aqueous Solution.

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Molecular dynamics simulations of kinetic isotope fractionation during the diffusion of ionic species in liquid water

Interpretation of isotope ratios, a powerful tool in geochemical investigations of fluid-rock systems, requires an understanding of all relevant processes that fractionate isotopes. One such process, diffusion in liquid water, has remained problematic despite its potential significance as a major cause of kinetic isotope fractionation. Recent laboratory experiments published by [Richter, F. M., Mendybaev, R. A., Christensen, J. N., Hutcheon, I. D., Williams, R. W., Sturchio, N. C., and Beloso Jr., A. D. (2006) Kinetic isotopic fractionation during diffusion of ionic species in water. Geochim. Cosmochim. Acta 70, 277–289.] have shown clearly for the first time that lithium and chloride isotopes are fractionated by diffusion in liquid water, whereas magnesium isotopes are not. In the present paper, we present the results of molecular dynamics simulations of lithium, chloride, and magnesium diffusion in liquid water that were designed to provide molecular-scale insight into the experimental findings of Richter et al. (2006). Our results indicate that the self-diffusion coefficients of lithium, chloride, and magnesium isotopes follow an inverse power-law dependence on ion mass ( D i ∝ m i - β , where D i is the self-diffusion coefficient of a solute with isotopic mass m i ). The power-law exponents ( β) deduced for lithium, chloride, and magnesium from the diffusivity data of Richter et al. (2006) are consistent with the mass dependencies found in our simulations. Further analysis of our simulation results showed that the experimental β-values are inversely related to the residence times of water molecules in the first solvation shells of the diffusing ions, as expected from mode-coupling and renormalized kinetic theories.

A Combined QM/MM Molecular Dynamics Simulations Study of Nitrate Anion (NO3-) in Aqueous Solution

The structural and dynamical properties of NO3- in dilute aqueous solution have been investigated by means of two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely HF/MM and B3LYP/MM, in which the ion and its surrounding water molecules were treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set. On the basis of both HF and B3LYP methods, a well-defined first hydration shell of NO3- is obtainable, but the shell is quite flexible and the hydrogen-bond interactions between NO3- and water are rather weak. With respect to the detailed analysis of the geometrical arrangement and vibrations of NO3-, the experimentally observed solvent-induced symmetry breaking of the ion is well reflected. In addition, the dynamical information, i.e., the bond distortions and shifts in the corresponding bending and stretching frequencies as well as the mean residence time of water molecules surrounding the NO3- ion, clearly indicates the "structure-breaking" ability of this ion in aqueous solution. From a methodical point of view it seems that both the HF and B3LYP methods are not too different in describing this hydrated ion by means of a QM/MM simulation. However, the detailed analysis of the dynamics properties indicates a better suitability of the HF method compared to the B3LYP-DFT approach.

Water properties inside nanoscopic hydrophobic pocket studied by computer simulations

The structure and dynamics of water in the vicinity of the hemispherical hydrophobic pocket of 8 A radius were examined via molecular dynamics simulations in NVT ensemble. Density, hydrogen bonding properties, and residence times of water molecules were projected on two-dimensional planes providing a spatial description of water behavior. We found that the average water density is significantly depleted relative to bulk value. A detailed analysis of pocket occupancy revealed fluctuations between states of completely empty pocket and a pocket filled with a bulklike fluid, which seem to result from collective behavior of water molecules. Free energy differences accompanying these fluctuations are rather small, suggesting that the given pocket radius is close to the critical one for transition between gas and liquid phases in the considered system. We show that the situation is different in the case of a simple Lennard-Jones fluid. These results indicate that changing the surface curvature from flat to concave may lead to qualitative difference in water behavior in its vicinity. We think that our studies may also put some light on binding site desolvation process which is necessary to understand to make correct predictions of binding energies.

Ab initio QM/MM dynamics of H3O+ in water

A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6-8 water molecules. It is treated at the Hartree-Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O4+) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O2+) structure. Besides the three nearest-neighbor water molecules directly hydrogen-bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ion's hydration shell indicate that such next-nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton.

Simulation studies of the protein-water interface. II. Properties at the mesoscopic resolution

We report molecular dynamics (MD) simulations of three protein-water systems (ubiquitin, apo-calbindin D(9K), and the C-terminal SH2 domain of phospholipase C-gamma1), from which we compute the dielectric properties of the solutions. Since two of the proteins studied have a net charge, we develop the necessary theory to account for the presence of charged species in a form suitable for computer simulations. In order to ensure convergence of the time correlation functions needed for the analysis, the minimum length of the MD simulations was 20 ns. The system sizes (box length, number of waters) were chosen so that the resulting protein concentrations are comparable to experimental conditions. A dielectric component analysis was carried out to analyze the contributions from protein and water to the frequency-dependent dielectric susceptibility chi(omega) of the solutions. Additionally, an even finer decomposition into protein, two solvation shells, and the remaining water (bulk water) was carried out. The results of these dielectric decompositions were used to study protein solvation at mesoscopic resolution, i.e., in terms of protein, first and second solvation layers, and bulk water. This study, therefore, complements the structural and dynamical analyses at molecular resolution that are presented in the companion paper. The dielectric component contributions from the second shell and bulk water are very similar in all three systems. We find that the proteins influence the dielectric properties of water even beyond the second solvation shell, in agreement with what was observed for the mean residence times of water molecules in protein solutions. By contrast, the protein contributions, as well as the contributions of the first solvation shell, are system specific. Most importantly, the protein and the first water shell around ubiquitin and apo-calbindin are anticorrelated, whereas the first water shell around the SH2 domain is positively correlated.

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.

Specific Effects of Divalent Cation Nitrates on the Nanotribology of Silica Surfaces

Recent investigations have shown that hydrated layers of monovalent cations adsorbed on silica (Donose, B. C.; Vakarelski, I. U.; Higashitani, K. Silica surfaces lubrication by hydrated cations adsorption from electrolyte solutions. Langmuir 2005, 21, 1834) or mica (Raviv, U.; Klein, J. Fluidity of bound hydration layers. Science 2002, 297, 1540) surfaces can act as highly efficient boundary lubricants. Here, by using the lateral force microscopy (LFM) mode of atomic force microscopy (AFM), we extended these investigations to the case of divalent cations, measuring the frictional force between a completely hydrophilic silica particle and a silica wafer in Ba2+, Sr2+, Ca2+, and Mg2+ nitrate solutions. The measurements demonstrated strong lubrication effects for solutions of Ba2+, Sr2+, and Ca2+ nitrates starting even at a very low electrolyte concentration, such as 3 × 10-5 M. As for Mg2+ ions, however, it is surprising to know that the frictional force increases with increasing electrolyte concentration. Possible nanotribological mechanisms are discussed, and the value of friction was found to be more closely related to the average residence time of water molecules around cations than to the number of water molecules in their hydration shell.

Dynamics of Halide Ion−Water Hydrogen Bonds in Aqueous Solutions: Dependence on Ion Size and Temperature

We have carried out a series of molecular dynamics simulations to investigate the dynamics of X(-)-water (X = F, Cl, Br, and I) and water-water hydrogen bonds in aqueous alkali halide solutions at room temperature and also of Cl(-)-water and water-water hydrogen bonds at seven different temperatures ranging from 238 to 318 K. The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The results of the hydrogen bond dynamics are obtained for two different cutoff values for the angular criterion. In both cases, similar dynamical behavior of the hydrogen bonds is found with respect to their dependence on ion size and temperature. The fluoride ion-water hydrogen bonds are found to break at a much slower rate than water-water hydrogen bonds, while the lifetimes of chloride and bromide ion-water hydrogen bonds are found to be shorter than those of fluoride ion-water ones but still longer than water-water hydrogen bonds. The short-time dynamics of iodide ion-water hydrogen bonds is found to be slightly faster, while its long-time dynamics is found to be slightly slower than the corresponding water-water hydrogen bond dynamics. Correlations of the observed dynamics of anion(water)-water hydrogen bonds with those of rotational and translational diffusion and residence times of water molecules in ion(water) hydration shells are also discussed. With variation of temperature, the lifetimes of both Cl(-)-water and water-water hydrogen bonds are found to show Arrhenius behavior with a slightly higher activation energy for the Cl(-)-water hydrogen bonds.

The dynamics of the solvation of Pb(II) in aqueous solution obtained by an ab initio QM/MM MD approach

Dynamic properties of the hydrated Pb(II) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at Hartree Fock quantum mechanical level. Librational as well as vibrational motions of first and second shell and the bulk as well as the frequencies of rotations have been evaluated by means of velocity auto correlation functions (VACF). The time evolution of the Pb–O distances and selected O–Pb–O angles in the first shell was evaluated. A lower limit of the mean ligand residence time of water molecules in the first shell was estimated as 0.23 ns, in the second shell a mean residence time of 5.6 ps was observed.

Ion solvation in aqueous supercritical electrolyte solutions at finite concentrations: a computer simulation study

A series of results from computer simulations of sodium chloride ionic solutions at both supercritical and ambient conditions are presented. We considered infinite dilute and finite concentration solutions (m=1, 2, 4 mol kg−1) at variable densities. Structure of water around ionic species is carefully analyzed. Special attention is devoted to the effects of ion pairing and clustering. Running coordination numbers and residence times of water molecules are also reported

Structure and dynamics of hydrated NH: An ab initio QM/MM molecular dynamics simulation

A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to investigate solvation structure and dynamics of NH(4) (+) in water. The most interesting region, the sphere includes an ammonium ion and its first hydration shell, was treated at the Hartree-Fock level using DZV basis set, while the rest of the system was described by classical pair potentials. On the basis of detailed QM/MM simulation results, the solvation structure of NH(4) (+) is rather flexible, in which many water molecules are cooperatively involved in the solvation shell of the ion. Of particular interest, the QM/MM results show fast translation and rotation of NH(4) (+) in water. This phenomenon has resulted from multiple coordination, which drives the NH(4) (+) to translate and rotate quite freely within its surrounding water molecules. In addition, a "structure-breaking" behavior of the NH(4) (+) is well reflected by the detailed analysis on the water exchange process and the mean residence times of water molecules surrounding the ion.

Molecular Dynamics Simulation of a Perylene-Derivative Langmuir Film

We performed a series of molecular dynamics simulations of an N,N'-di-n-butyl-3,4:9,10-perylene tetracarboxydiimide (BuPTCD) Langmuir film. The film was studied at three surface areas (0.38, 0.40, and 0.45 nm2 molecule(-1)) using model systems consisting of one BuPTCD monolayer on each side of a 6.0-nm-thick water slab. On the basis of geometrical reasoning and surface pressure results, it was found that perylene molecules seem to be oriented mainly head-on toward the water surface. On the other hand, the average orientation of the perylene tetracarboxidiimide moiety during simulations indicated that molecular alignment is not simple, changing from tilted face-on to tilted head-on during compression. The change in orientation of BuPTCD molecules was accompanied by the thickening of the film as the area decreased. Films also became more orderly at small surface areas, mostly at the rigid perylene core. BuPTCD molecules are not evenly hydrated, with very few solvent molecules hydrating the hydrophobic tails, whereas a considerable number of water molecules were hydrogen bonded to diimide oxygen atoms. Besides, the residence times of water molecules around perylene atomic sites increased from the terminal methyl groups to the diimide oxygen atoms. Finally, the electric potential profile across the monolayer was found to depend on the area occupied by each molecule, indicating that properties of the films may vary considerably with the area occupied by each molecule. Altogether, the molecular description arising from our computer simulations suggests which structural patterns may be found in these films depending on the surface density of perylene molecules.

Ab initio QM/MM dynamics of anion–water hydrogen bonds in aqueous solution

Dynamical properties of F −–water and Cl −–water hydrogen bonds in aqueous solution have been studied by ab initio QM/MM molecular dynamics simulations, in which the whole first hydration sphere of the anion was treated at Hartree–Fock level using D95V+, 6-31+G and D95V++ basis sets for F −, Cl − and water, respectively. According to a detailed analysis of the bond distortions and shifts in the corresponding bending and stretching frequencies as well as the mean residence times of water molecules surrounding the ions, F − clearly acts as a ‘structure-maker’, while Cl − solvation leads to a more flexible structure with frequent re-arrangements of the hydrogen bonds.

Conformational Transitions in Eosinophil Cationic Protein: A Molecular Dynamics Study in Aqueous Environment

Extensive molecular dynamics simulations have been performed on eosinophil cationic protein (ECP). The two structures found in the crystallographic dimer (ECPA and ECPB) have been independently simulated. A small difference in the pattern of the sidechain hydrogen bonds in the starting structure has resulted in interesting differences in the conformations accessed during the simulations. In one simulation (ECPB), a stable equilibrium conformation was obtained and in the other (ECPA), conformational transitions at the level of sidechain interactions were observed. The conformational transitions exhibit the involvement of the solvent (water) molecules with a pore-like construct in the equilibrium conformation and an opening for a large number of water molecules during the transition phase. The details of these transitions are examined in terms of intra-protein hydrogen bonds, protein-water networks and the residence times of water molecules on the polar atoms of the protein. These properties show some significant differences in the region between the N-terminal helix and the loop before the C-terminal strand as a function of different conformations accessed during the simulations. However, the stable hydrogen bonds, the protein-water networks, and the hydration patterns in most part of the protein including the active site are very much similar in both the simulations, indicating the fact that these are intrinsic properties of proteins.

Water network dynamics at the critical moment of a peptide's beta-turn formation: a molecular dynamics study.

All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of beta-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable beta-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the beta-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the beta-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of beta-turns.

Structure and dynamics of Au+ ion in aqueous solution: ab initio QM/MM MD simulations.

Structure and dynamics of hydrated Au(+) have been investigated by means of molecular dynamics simulations based on ab initio quantum mechanical molecular mechanical forces at Hartree-Fock level for the treatment of the first hydration shell. The outer region of the system was described using a newly constructed classical three-body corrected potential. The structure was evaluated in terms of radial and angular distribution functions and coordination number distributions. Water exchange processes between coordination shells and bulk indicate a very labile structure of the first hydration shell whose average coordination number of 4.7 is a mixture of 3-, 4-, 5-, 6-, and 7-coordinated species. Fast water exchange reactions between first and second hydration shell occur, and the second hydration shell is exceptionally large. Therefore, the mean residence time of water molecules in the first hydration shell (5.6 ps/7.5 ps for t*= 0.5 ps/2.0 ps) is shorter than that in the second shell (9.4 ps/21.2 ps for t*= 0.5 ps/2.0 ps), leading to a quite specific picture of a "structure-breaking" effect.

Density and temperature effects on the orientational and dielectric properties of supercritical water.

The influence of temperature and density changes on the reorientational motions and dielectric properties of supercritical water is investigated by molecular dynamics simulations. A rigid simple point charged potential has been used to model water-water interactions. This model has revealed to be very satisfactory to reproduce thermodynamic, diffusive, and static dielectric properties of supercritical water. Reorientation times of water molecules have been computed along specific molecular directions and compared with available experimental data. The imaginary part of the frequency dependent dielectric constant, spectral densities of states, and residence times of water molecules in their first hydration shells are also evaluated.