Mean Number Of Hydrogen Bonds Research Articles

Artificial Water Channels—Progress Innovations and Prospects

Artificial Water Channels—Progress Innovations and Prospects

Computer simulation study of ion-water and water-water hydrogen bonds in sulfuric acid solutions at low temperatures

Molecular dynamics simulations of sulfuric acid solutions at several temperatures (230, 250, 273 and 298 K) and concentrations (10, 20, 30 and 40 wt%) have been carried out. The dissociation of the acid has been explicitly considered, in accordance with the available experimental measurements. So, the simulated systems are made up of the following molecular constituent species: water molecules, hydronium cations, bisulfate anions and sulfate dianions. Calculations have been conducted using a reliable force field, which allows us to determine density and viscosity values, which are in a reasonably good agreement with the available experimental data in the temperature and concentration ranges considered in this work. Simulations have also been employed to determine the radial distribution functions, which involve water molecules, and the diffusion coefficients of the constituent species. Moreover, a hydrogen bond analysis, involving only water molecules, has also been fulfilled. To this end, the mean number of hydrogen bonds between water molecules and between ions and water molecules, the percentages of molecular species hydrogen bonded with a given number of water molecules, and the continuous and interrupted lifetimes have been calculated. We observe that most properties are mainly sensitive to the concentration. We also notice that water molecules bonded to the anions are more labile than those bonded to other water molecules or to hydronium ions, the labilities increasing when the temperature rises. Moreover, the characteristic tetrahedral structure of water vanishes when the concentration or the temperatures increases. In the first case because water molecules tend to bond to a larger number of ions. In the second because the mean number of hydrogen bonds between water molecules and their lifetimes decrease. Finally, we also estimate the activation energies from the interrupted lifetimes, the viscosity and the diffusion coefficients. We note that these energies are very similar and they increase when the concentration rises.

Identification of plant α-tubulin amino acids playing a key role in specific binding of nitroaniline compounds

Aim. Computational prediction of amino acid residues critical for specific binding of nitro- and dinitroaniline compounds in plant α-tubulin. Methods. Protein structure modeling (I-Tasser, Grid-computing) and ligand library preparation, molecular docking (CCDC Gold), molecular dynamics (MD, Gromacs computing in Grid). Evaluation of the amino acid ensemble associated with ligand binding based on results of MD energy perturbations of protein-ligand complex. Results. The structural model of plant α-tubulin from Avena sativa was build. Also, the virtual library of 25 nitroaniline compounds was prepared. The docking of ligands into the interdimer contact of α-tubulin and MD simulations of the leading complexes reveal differences in ligands conformational energy during the exchange between free and binding states. The mean number of hydrogen bonds and dynamics of their formation in complex were compared. These computations allow us to select a.a. residues playing key role in specific interaction with nitro- and dinitroaniline compounds in plant α-tubulin. Conclusions. Computational prediction specify 28 a.a. residues playing the main role in binding of nitro- and dinitroaniline compounds with plant α-tubulin from Avena sativa: Arg2, Glu3, Ile4, Cys129, Thr130, Gly131, Leu132, Gln133, Gly134, Gly162, Lys163, Lys164, Ser165, Leu242, Arg243, Asp245, Gly246, Ala247, Ile248, Asn249, Val250, Asp251,Val252, Thr253, Glu254, Phe255, Thr257, Asn258.
 Keywords: plant, α-tubulin, nitroaniline compounds, molecular docking, molecular dynamics, ligand binding.

Water-water and ion-water hydrogen bonding in sulfuric acid solutions

Molecular dynamics simulations of sulfuric acid solutions at room temperature and at concentrations up to 40 wt% have been performed. The dissociation of the acid in water has been implicitly taken into account by assuming that the simulated systems are made up of the following molecular constituent species: water molecules, hydronium cations, bisulfate anions and sulfate dianions. Calculations have been carried out using a reliable force field which provides a good agreement between the experimental and the simulation densities and viscosity coefficients. The density and several structural and dynamical quantities, such as the radial distribution functions, the shear viscosity and the diffusion coefficients, have been calculated. The results show a noticeable good agreement with the available experimental data. A study of the hydrogen bonding which involve water molecules has also been performed. Then, the mean number of hydrogen bonds between water molecules and between ions and water molecules, and the percentages of these hydrogen bonds per water molecule or ion have been computed. Moreover, an analysis of the formation and rupture of the hydrogen bonds has also been made. To this end, the continuous and the interrupted hydrogen bond lifetimes have been calculated. Our findings suggest that the water molecules hydrogen bonded to the anions are more labile than those bonded to other water molecules or to hydronium ions. Finally, the role played by the acid concentration on these quantities has also been analyzed. Then, for instance, an increase of the lability of the water molecules, which are hydrogen bonded to other water molecules, has been observed when the concentration rises.

Interaction between hydroxyl group and water saturated supercritical CO 2 revealed by a molecular dynamics simulation study

Molecular dynamics simulations were performed to investigate hydroxyl groups-CO2 interactions. Three silica surfaces with different hydroxyl group structures were selected and the effect of pressure was studied in the range of 4.8–32.6 MPa. Radial distribution functions especially for OsOc pair show evidence for hydrogen bonds between hydroxyl groups and CO2 molecules. The hydrogen bonds structure was analyzed using the mean number of hydrogen bonds. Pressure and hydroxyl group structures were found to affect H-bonding structure. These findings provide new insight for CO2-hydroxyl group interactions to better understand the effects of CO2 in carbon capture and sequestration process.

Hydrogen bonds at silica–CO2 saturated water interface under geologic sequestration conditions

ABSTRACTTo investigate the effects of sequestration condition on hydrogen bonds between mineral and water, molecular dynamics simulations have been performed. The simulations were conducted at conditions related with geologic sequestration sites: pressure (3.1–32.6 MPa), temperature (318 and 383 K), salinity (0–3 M), salt (NaCl and CaCl2) and silica surface models Q2 (geminal), Q3 (isolated) and amorphous Q3. The hydrogen bonds were classified into four types: silica–silica, silica–dissolved CO2, silica–water as donors and silica–water as acceptors. The mean numbers of hydrogen bonds for each type were analysed. The results show that: (1) silica surface silanol groups do not form H-bonds with dissolved CO2 molecules in water (brine); (2) The mean number of hydrogen bonds between silanol groups follows the order: Q2 > amorphous Q3 > Q3; (3) The mean number of hydrogen bonds between silanol and water molecules follows the order: Q3 > amorphous Q3 > Q2.

Diffusion of Hydration Water around Intrinsically Disordered Proteins.

Hydration water dynamics around globular proteins have attracted considerable attention in the past decades. This work investigates the hydration water dynamics around partially/fully intrinsically disordered proteins and compares it to that of the globular proteins via molecular dynamics simulations. The translational diffusion of the hydration water is examined by evaluating the mean-square displacement and the velocity autocorrelation function, while the rotational diffusion is probed through the dipole-dipole time correlation function. The results reveal that the translational and rotational motions of water molecules at the surface of intrinsically disordered proteins/regions are less restricted as compared to those around globular proteins/ordered regions, which is reflected in their higher diffusion coefficient and lower orientational relaxation time. The restricted mobility of hydration water in the vicinity of the protein leads to a sublinear diffusion in a heterogeneous interface. A positive correlation between the mean number of hydrogen bonds and the diffusion coefficient of hydration water implies higher mobility of water molecules at the surface of disordered proteins, which is due to their higher number of hydrogen bonds. Enhanced hydration water mobility around disordered proteins/regions is also related to their higher hydration capacity, low hydrophobicity, and increased internal protein motions. Thus, we generalize that the intrinsically disordered proteins/regions are associated with higher hydration water mobility as compared to globular protein/ordered regions, which may help to elucidate their varied functional specificity.

Estimation of the Mutual Orientation and Intermolecular Interaction of C12Ex from Molecular Dynamics Simulations

Nonionic surfactants, such as poly(ethylene glycol) alkyl ethers (abbreviated as CyEx) show a rich phase behavior in aqueous solution, i.e., they form micellar, lamellar, cubic, and so forth phases depending on experimental parameters such as the hydrophobic and hydrophilic chain lengths, temperature, or concentration. The aim of the present study is to determine the nature of the preaggregates, which are inferred to exist before the actual self-assembly process in aqueous solution, and to assess the aptitude to their formation. The target molecules are C12E3, C12E4 and C12E5, surfactants of moderate water solubility. Coarse-grained and all-atom molecular dynamics simulations (NPT/293 K) of two molecules of each species with explicit water in periodic boundary conditions are carried out to estimate the mutual orientation and the interaction between the surfactants in their dimers. The force fields are MARTINI and Amber99, the latter with self-derived parameters for the ether groups. The change in the orientation and distance between the molecules in the dimers are discussed based on different structural parameters. In addition, the interaction between the surfactants is evaluated from quantum chemistry calculations in terms of binding energy for the average structures from the cluster analysis. The solvent-solute interaction is quantified by the mean number of hydrogen bonds formed between them. On the basis of combined analysis, a series of different structures for subsequent study of the possible self-assembly patterns of C12E3, C12E4, and C12E5 is outlined.

A molecular dynamics study of cryoprotective agent – Water–sodium chloride ternary solutions

Molecular dynamics simulation method has been used to study the characteristics of cryoprotective agent (CPA) solutions with glycerol as a CPA at normal and subzero temperatures. Radial distribution functions have been calculated. The geometrical criterion has been used to analyze hydrogen bonding network and dynamics. It has been found that the mean number of hydrogen bonds per oxygen atom decreases as glycerol concentration increases. The mean number of hydrogen bonds per hydrogen atom show little dependence on solute concentration. The mean number of hydrogen bonds per water molecule decreases as solute concentration increases. The relaxation time and the hydrogen bonding lifetime show tendencies of increasing as solute concentration increases. The lifetimes of hydrogen bonds between water molecules are smaller than those between glycerol and water molecules. The hydration numbers of sodium cation and chlorine anion and water self-diffusion coefficients have also been reported. The results have been used to analyze the protection of cryoprotective agent.

Structural properties of water: Comparison of the SPC, SPCE, TIP4P, and TIP5P models of water

Molecular-dynamics simulations were carried out for the SPC, SPCE, TIP4P, and TIP5P models of water at 298 K. From these results we determine the following quantities: the absolute entropy using the two-particle approximation, the mean lifetime of the hydrogen bond, the mean number of hydrogen bonds per molecule, and the mean energy of the hydrogen bond. From the entropy calculations we find that nearly all contributions to the total entropy originates from the orientation effects. Moreover, we determine the contributions to the total entropy which originate from the first, second, and higher solvation shells. It is interesting that the limits between solvation shells are clearly visible. The first solvation shell (0.22 < r < 0.36 nm) contributes approximately 43 J mol K to the total entropy; the second solvation shell (0.36 < r < 0.60 nm) contributes approximately 12 J mol K, while contributions from the third and other solvation shells are very small, approximately 2 J mol K in summary. This indicates that water molecules are strongly ordered up to 0.55-0.6 nm around the central water molecule, and beyond this limit the ordering diminishes. The results of calculations (entropy and hydrogen bonds) are compared with the experimental data for the choosing of the best water model. We find that the SPC and TIP4P models reproduce the best experimental values, and we recommend these models for computer simulations of the aqueous solution of biomolecules.

Anomalous Density and Permittivity Effects on the Structure of Water

The relationship between the structural peculiarities of the hydrogen bond net and the anomalous behavior of density and dielectric permittivity of water is investigated. The degree of ordering in the network of hydrogen bonds is described in terms of the structural functions, among which the most important ones are tetrahedricity and the mean number of hydrogen bonds per molecule. The temperature dependence of the number of hydrogen bonds per molecule is discussed in terms of the analysis of the experimental temperature dependences of density and permittivity of water on the saturation line. The estimated density of hexagonal ice at the melting point is reproduced in terms of the concepts suggested for analysis; the estimate is rather close to the experimental value. Possible applications of the new approach are discussed.

Are There Hydrogen Bonds in Supercritical Water?

The proton NMR chemical shift has been measured for water from 25 to 600 °C and from 1 to 400 bar, conditions extending well beyond the critical point. Dilute solutes were employed as chemical shift references to avoid the effect of the varying magnetic susceptibility. The large changes in chemical shift (4.1 ppm) are interpreted as changes in the hydrogen bond network, because all other intermolecular interactions are known to result in much smaller effects. Using a linear relation between chemical shift and the mean number of hydrogen bonds, the NMR results show there are still 29% as many hydrogen bonds at 400 °C and 400 bar (ρ = 0.52 g/cm3 ) as for room temperature water. The present results are compared to other measurements and calculations.

Magnetic Treatment of Water: Possible Mechanismsand Conditions for Applications

In this paper, fundamental properties and parameters of water molecules, fine “structure” of water, hydration of ions and nature of the hydrogen bond are reviewed. A model is outlined of possible mechanisms of the effect of relatively weak magnetic fields on the statistically mean number of hydrogen bonds between water molecules, as a result of forbidden triplet—singlet transitions in the Zeeman electron—proton multiplets of the water molecule and its near surroundings. The effect of the influence of the magnetic field on the ion—colloidal subsystems of aqueous environment are analysed. It is shown that the energy of magnetic dipole interaction of colloidal particles of the magnetite type is sufficient for their flocculation and concentration in areas of high gradient of the magnetic field, and for their stability against hydrodynamic disruption of the flocs, possible centres of crystallisation of CaCO3 On the basis of the proposed calculations, and also based on data presented by other authors,particularly from ex—Soviet Union, conditions and regimes of anti—scale magnetic treatment of water are reviewed.