First Shell Of Hydration Research Articles

Interaction Energy Analysis of Monovalent Inorganic Anions in Bulk Water Versus Air/Water Interface.

Soft anions exhibit surface activity at the air/water interface that can be probed using surface-sensitive vibrational spectroscopy, but the structural implications of this surface activity remain a matter of debate. Here, we examine the nature of anion–water interactions at the air/water interface using a combination of molecular dynamics simulations and quantum-mechanical energy decomposition analysis based on symmetry-adapted perturbation theory. Results are presented for a set of monovalent anions, including Cl−, Br−, I−, CN−, OCN−, SCN−, , , and (), several of which are archetypal examples of surface-active species. In all cases, we find that average anion–water interaction energies are systematically larger in bulk water although the difference (with respect to the same quantity computed in the interfacial environment) is well within the magnitude of the instantaneous fluctuations. Specifically for the surface-active species Br−(aq), I−(aq), (aq), and SCN−(aq), and also for ClO−(aq), the charge-transfer (CT) energy is found to be larger at the interface than it is in bulk water, by an amount that is greater than the standard deviation of the fluctuations. The Cl−(aq) ion has a slightly larger CT energy at the interface, but (aq) does not; these two species are borderline cases where consensus is lacking regarding their surface activity. However, CT stabilization amounts to <20% of the total induction energy for each of the ions considered here, and CT-free polarization energies are systematically larger in bulk water in all cases. As such, the role of these effects in the surface activity of soft anions remains unclear. This analysis complements our recent work suggesting that the short-range solvation structure around these ions is scarcely different at the air/water interface from what it is in bulk water. Together, these observations suggest that changes in first-shell hydration structure around soft anions cannot explain observed surface activities.

A DFT study on the speciation of aqueous gold and copper cyanide complexes

The speciation of copper and gold cyanide complexes was investigated using Density Functional Theory (DFT) in order to understand the behaviour of these complexes in aqueous solutions. To represent the local environment, two methods of implicit (COSMO) and explicit water molecules were utilized and the results were compared to evaluate their capability. The hydration state of the species, stability constants, cluster formation, interaction of different species and finally the gold leaching character of copper cyanide complexes were investigated in details.The solvation energy of Au(CN)2−, Cu(CN)2−, Cu(CN)3−2 and Cu(CN)4−3 were calculated as −41.1, −42.5, −98.1 and −168.7 kcal·mol−1 with 4, 4, 6 and 8 water molecules in the first shell of hydration, respectively. A high level of cluster formation was observed for both dicyano copper and gold complexes. Cu(CN)2− displayed the highest level of interaction with Au(CN)2− and mixed cluster formation of dicyano complexes was proposed as a mechanism of copper cyanide adsorption on the activated carbon. Other species including tri and tetracyano complexes were found to be well dispersed with minimal interaction with other species. The leaching potential of copper cyanide complexes was proved by computational modelling for the first time, here. Cyanide ions are released from all three different order copper cyanide complexes, while only released CN− from Cu(CN)3−2 and Cu(CN)4−3 dissolves gold and Cu(CN)2− passivates the gold surface by formation of Au(CN)-Cu(CN) layer. The results of this computational modelling study can be used in providing a more in depth understanding of the chemistry of gold hydrometallurgy in the presence of other metal ions.

Development of Lennard-Jones and Buckingham Potentials for Lanthanoid Ions in Water.

New sets of Lennard-Jones and Buckingham potentials have been developed to be used in classical molecular dynamics simulations of Ln3+-containing systems for the whole lanthanoid series. The force-field parameters have been refined by directly comparing the hydration structure obtained from the simulations with the extended X-ray absorption fine structure (EXAFS) experimental data, in order to reproduce Ln3+-water EXAFS experimentally inferred mean distances. Analysis of the simulation results has shown that both Lennard-Jones and Buckingham potentials are able to properly describe the radial distribution of water molecules around the Ln3+ ions, the smooth decrease of the hydration number along the lanthanoid series, as well as the geometry of the first-shell hydration complex formed by Ln3+ ions in water. The newly optimized interaction potential parameters can be used in conjunction with force fields available in the literature to investigate the solvation properties of Ln3+ ions in different disordered systems.

Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction

We carried out a prospective evaluation of the utility of the SIE (solvation interaction energy) scoring function for virtual screening and binding affinity prediction. Since experimental structures of the complexes were not provided, this was an exercise in virtual docking as well. We used our exhaustive docking program, Wilma, to provide high-quality poses that were rescored using SIE to provide binding affinity predictions. We also tested the combination of SIE with our latest solvation model, first shell of hydration (FiSH), which captures some of the discrete properties of water within a continuum model. We achieved good enrichment in virtual screening of fragments against trypsin, with an area under the curve of about 0.7 for the receiver operating characteristic curve. Moreover, the early enrichment performance was quite good with 50% of true actives recovered with a 15% false positive rate in a prospective calculation and with a 3% false positive rate in a retrospective application of SIE with FiSH. Binding affinity predictions for both trypsin and host-guest complexes were generally within 2 kcal/mol of the experimental values. However, the rank ordering of affinities differing by 2 kcal/mol or less was not well predicted. On the other hand, it was encouraging that the incorporation of a more sophisticated solvation model into SIE resulted in better discrimination of true binders from binders. This suggests that the inclusion of proper Physics in our models is a fruitful strategy for improving the reliability of our binding affinity predictions.

Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models

Next-generation solvation models are devised to mimic the accuracy and generality of explicit solvation models at the speed of current popular implicit solvation models. One such method is the first-shell of hydration (FiSH) continuum model that was trained on hydration energetics from LIE calculations and molecular dynamics simulations in explicit solvent. Here we tested prospectively the FiSH model on the SAMPL-3 hydration data set that zooms in the effect of chlorination on solvation. We compare these FiSH predictions with those from retrospective LIE calculations. We find that neither FiSH nor LIE can reproduce well the absolute values and the trend of hydration free energies in the biphenyl and dioxin aromatic chlorination series. Some of the hypotheses behind this performance are discussed and tested. The LIE explicit-solvent model shows some improvement relative to the FiSH continuum model, and we correct a systematic deviation in the continuum van der Waals term of FiSH associated with aromatic Cl atom type.

&lt;b&gt;Hydration structure and water exchange dynamics of Fe(II) ion in aqueous solution&lt;/b&gt;

Computer simulation studies of the hydration structure and water exchange dynamics in the first hydration shell for Fe(II) in water are presented. The structure of the hydrated ion is discussed in terms of radial distribution functions, coordination numbers, and angular distributions. The average first-shell hydration structure is a 6-coordinate octahedron, in agreement with experimental results. The water exchange reaction around the Fe(II) ion in water was investigated using classical umbrella-sampling molecular dynamic simulations. The water exchange mechanism, estimates for reaction rate, as well as structural changes during the activation process are discussed. The water exchange mechanism proceeds via the Id mechanism. The water exchange rate constant at 298 K is estimated by the transition state theory to be 2.1 x 107 s-1, assuming a transmission coefficient of unity. KEY WORDS: Hydration, Water exchange, Umbrella sampling, Rate constant, Iron(II) ion Bull. Chem. Soc. Ethiop. 2010, 24(2), 239-250.

Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model.

Local ordering of water in the first hydration shell around a solute is different from isotropic bulk water. This leads to effects that are captured by explicit solvation models and missed by continuum solvation models which replace the explicit waters with a continuous medium. In this paper, we introduce the First-Shell Hydration (FiSH) model as a first attempt to introduce first-shell effects within a continuum solvation framework. One such effect is charge asymmetry, which is captured by a modified electrostatic term within the FiSH model by introducing a nonlinear correction of atomic Born radii based on the induced surface charge density. A hybrid van der Waals formulation consisting of two continuum zones has been implemented. A shell of water restricted to and uniformly distributed over the solvent-accessible surface (SAS) represents the first solvation shell. A second region starting one solvent diameter away from the SAS is treated as bulk water with a uniform density function. Both the electrostatic and van der Waals terms of the FiSH model have been calibrated against linear interaction energy (LIE) data from molecular dynamics simulations. Extensive testing of the FiSH model was carried out on large hydration data sets including both simple compounds and drug-like molecules. The FiSH model accurately reproduces contributing terms, absolute predictions relative to experimental hydration free energies, and functional class trends of LIE MD simulations. Overall, the implementation of the FiSH model achieves a very acceptable performance and transferability improving over previously developed solvation models, while being complemented by a sound physical foundation.

Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge

The SAMPL2 hydration free energy blind prediction challenge consisted of a data set of 41 molecules divided into three subsets: explanatory, obscure and investigatory, where experimental hydration free energies were given for the explanatory, withheld for the obscure, and not known for the investigatory molecules. We employed two solvation models for this challenge, a linear interaction energy (LIE) model based on explicit-water molecular dynamics simulations, and the first-shell hydration (FiSH) continuum model previously calibrated to mimic LIE data. On the 23 compounds from the obscure (blind) dataset, the prospectively submitted LIE and FiSH models provided predictions highly correlated with experimental hydration free energy data, with mean-unsigned-errors of 1.69 and 1.71 kcal/mol, respectively. We investigated several parameters that may affect the performance of these models, namely, the solute flexibility for the LIE explicit-solvent model, the solute partial charging method, and the incorporation of the difference in intramolecular energy between gas and solution phases for both models. We extended this analysis to the various chemical classes that can be formed within the SAMPL2 dataset. Our results strengthen previous findings on the excellent accuracy and transferability of the LIE explicit-solvent approach to predict transfer free energies across a wide spectrum of functional classes. Further, the current results on the SAMPL2 test dataset provide additional support for the FiSH continuum model as a fast yet accurate alternative to the LIE explicit-solvent model. Overall, both the LIE explicit-solvent model and the FiSH continuum solvation model show considerable improvement on the SAMPL2 data set over our previous continuum electrostatics-dispersion solvation model used in the SAMPL1 blind challenge.

Quantum mechanical/molecular mechanical molecular dynamic simulation of zinc(II) ion in water

The hydration structure of the Zn(II) ion has been studied by classical molecular dynamics (CMD) and quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations, using newly constructed ab initio two-body potentials and a three-body correction function. The average first-shell hydration structure is a 6-coordinate octahedron, and the structure parameters obtained by the QM/MM-MD simulation are in reasonable agreement with the experimental values. The first-shell angular distribution functions show a satisfactory consistency for both simulations, suggesting that the classical potential functions well describe the O–Zn–O angular distortion in the CMD simulation, while the quantum mechanical treatment of the Zn(II) ion and its first hydration shell in the QM/MM-MD simulation increases the tilting probability of the coordinating H 2O molecules. Dynamic properties such as vibrational and rotational motions of water molecules were evaluated using velocity autocorrelation functions (VACFs).

Many-Body Effects in Combined Quantum Mechanical/Molecular Mechanical Simulations of the Hydrated Manganous Ion

Two different quantum mechanics/molecular mechanics molecular dynamics simulation techniques (QM/MM-MD) are compared using as an example the hydrated manganous ion. One includes a perturbation field composed of point charges representing the bulk solvent molecules polarizing the QM region in addition to a quantum chemically derived two-body potential. The other includes the two-body potential plus a three-body correction function. In both simulations, the QM region comprises the ion and its first hydration shell and hence includes all many-body terms up to the QM frontier. The structure of the hydrated ion is discussed in terms of radial distribution functions, coordination numbers, and angular distributions. The results show that both QM/MM-MD techniques agree well with experimental findings for the first-shell hydration structure. QM/MM-MD including point charges has been found to be a satisfactory and economic alternative in studying the first hydration shell without the need to undergo the time-consum...

Hydration dynamics of the collagen triple helix by NMR

The hydration of the collagen-like Ac-(Gly-Pro-Hyp)6-NH2 triple-helical peptide in solution was investigated using an integrated set of high-resolution NMR hydration experiments, including different recently developed exchange-network editing methods. This approach was designed to explore the hydration dynamics in the proximity of labile groups, such as the hydroxyproline hydroxyl group, and revealed that the first shell of hydration in collagen-like triple helices is kinetically labile with upper limits for water molecule residence times in the nanosecond to sub-nanosecond range. This result is consistent with a “hopping” hydration model in which solvent molecules are exchanged in and out of solvation sites at a rate that is not directly correlated to the degree of site localization. The hopping model thus reconciles the dynamic view of hydration revealed by NMR with the previously suggested partially ordered semi-clathrate-like cylinder of hydration. In addition, the nanosecond to sub-nanosecond upper limits for water molecule residence times imply that hydration-dehydration events are not likely to be the rate-limiting step for triple helix self-recognition, complementing previous investigations on water dynamics in collagen fibers. This study has also revealed labile proton features expected to facilitate the characterization of the structure and folding of triple helices in collagen peptides.

Comparison of two hydrated forms of sodium inosine 5'-monophosphate

The crystal and molecular structure of a decahydrated form of the sodium salt of inosine 5'-monophosphate (C10H12N4O8P-.Na+.10H2O) was solved to study the effect of hydration on the conformation of nucleic acids. Monoclinic, space group P2(1), a = 8.730 (3), b = 22.349 (7), c = 12.282 (4) A, beta = 109.68 (3) degrees, V = 2256.52 A3, Mr = 550.34, Z = 4, F(000) = 1196, Dx = 1.62 g cm-3, mu = 21.7 cm-1, lambda(Cu K alpha) = 1.54056 A, R = 0.070, wR = 0.102 for 3404 unique [Inet greater than 2 sigma (Inet)] observed reflections out of 3457 unique reflections. The two molecules (A and B) in the asymmetric unit differ in the arrangement of the first shell of hydration and in the torsion angles of the ribose and phosphate. The bond lengths and angles are similar to those of the structure of a less hydrated ('dry') form of the same nucleotide (C10H12N4O8P-.Na+.8H2O) determined previously in space group C222(1) [Rao & Sundaraligam (1969). J. Am. Chem. Soc. 91, 1210-1217]. The twofold symmetry in the 'dry' form is destroyed in the present crystal structure due to the relative displacement of the two independent molecules and reorganization of the hydration shell. Molecule A is different from (r.m.s. = 0.190 A) while molecule B is similar to (r.m.s. = 0.093 A) that of the 'dry' form. The conformation adopted is influenced mainly by the differences in the endocyclic torsion angles of the ribose.

Ordered water structure around a B-DNA dodecamer : A quantitative study

The crystal structure of the double-helical B-DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G has been solved and refined independently in three forms: (1) the parent sequence at room temperature; (2) the same sequence at 16 K; and (3) the 9-bromo variant C-G-C-G-A-A-T-T BrC-G-C-G at 7 °C in 60% (v/v) 2-methyl-2.4-pentanediol. The latter two structures show extensive hydration along the phosphate backbone, a feature that was invisible in the native structure because of high temperature factors (indicating thermal or static disorder) of the backbone atoms. Sixty-five solvent peaks are associated with the phosphate backbone, or an average of three per phosphate group. Nineteen other molecules form a first shell of hydration to base edge N and O atoms within the major groove, and 36 more are found in upper hydration layers. The latter tend to occur in strings or clusters spanning the major groove from one phosphate group to another. A single spermine molecule also spans the major groove. In the minor groove, the zig-zag spine of hydration that we believe to be principally responsible for stabilizing the B form of DNA is found in all three structures. Upper level hydration in the minor groove is relatively sparse, and consists mainly of strings of water molecules extending across the groove, with few contacts to the spine below. Sugar O-1′ atoms are closely associated with water molecules, but these are chiefly molecules in the spine, so the association may reflect the geometry of the minor groove rather than any intrinsic attraction of O-1′ atoms for hydration. The phosphate O-3′ and O-5′ atoms within the backbone chain are least hydrated of all, although no physical or steric impediment seems to exist that would deny access to these oxygen atoms by water molecules.

Hydration of the halide ions in certain organic solvents

The amount of water co-extracted by the halide anions into several solvents has been determined. The order was always Cl − > Br − > I −, and at high organic-phase salt concentrations, the hydration numbers increased with increasing concentration, apparently paralleling the formation of ion pairs and higher ion aggregates. In nitrobenzene the lower, limiting values are 3·3, 1·8, and 1·0 moles of water per anion for Cl −, Br −, and I −, respectively. With dichloroethane as solvent, and more particularly with chloroform, solvation of the anion by the (weakly) acid proton of the diluent replaces part of the hydration, and the hydration number observed decreases markedly. For a number of reasons, the hydration numbers observed are lower limits to the first-shell hydration or coordination number of the anion.