Exploring the capabilities of X-ray absorption spectroscopy for determining the structure of electrolyte solutions: computed spectra for Cr(3+) or Rh(3+) in water based on molecular dynamics

Extended X-ray absorption fine structure (EXAFS) spectra of Cr(3+) and Rh(3+) in aqueous solution are analyzed and compared with computed spectra derived from structural results obtained by molecular dynamics (MD) simulation. This procedure quantifies the reliability of the EXAFS structural determination when applied to ions in solution. It provides guidelines for interpreting experimental spectra of octahedrally coordinated metal cations in aqueous solution. A set of relationships among Debye-Waller factors is proposed on the basis of MD results to reduce the number of independent fit parameters. The determination of the second hydration shell is examined. Calculated XANES spectra compare well with experimental ones. Indeed, the splitting observed on the main peak of the Rh K-edge was anticipated by the calculations. Simulated spectra from MD structures of increasing cluster size show a relationship between the second hydration shell and features of the XANES region at energies just above the edge. The combination of quantum and statistical calculations with the XANES spectrum is found to be very fruitful to get insight into the quantitative estimation of structural properties of electrolyte solutions.     

Development and validation of an integrated computational approach for the study of ionic species in solution by means of effective two-body potentials. The case of Zn2+, Ni2+, and Co2+ in aqueous solutions

In this paper we have developed an effective computational procedure for the structural and dynamical investigation of ions in aqueous solutions. Quantum mechanical potential energy surfaces for the interaction of a transition metal ion with a water molecule have been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective ion-water interactions have been fitted by suitable analytical potentials, and have been utilized in molecular dynamics (MD) simulations to obtain structural and dynamical properties of the ionic aqueous solutions. This procedure has been successfully applied to the Co2+-H2O open-shell system and, for the first time, Co-oxygen and Co-hydrogen pair potential functions have been determined and employed in MD simulations. The reliability of the whole procedure has been assessed by applying it also to the Zn2+ and Ni2+ aqueous solutions, and the structural and dynamical properties of the three systems have been calculated by means of MD simulations and have been found to be in very good agreement with experimental results. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to extended X-ray absorption fine structure (EXAFS) experiments.     

Analysis and simulation of the structure of nanoparticles that undergo a surface-driven structural transformation

A room temperature solid-state structural transformation was observed in 3 nm ZnS nanoparticles in methanol following the addition of water (Zhang et al., Nature 424, 1025, 2003). Experimental wide angle x-ray scattering (WAXS), x-ray absorption near edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) spectroscopy measurements show a large increase in crystallinity associated with water addition, in agreement with molecular dynamics (MD) predictions. Here we perform first-shell EXAFS and pair distribution function analysis and whole-nanoparticle calculations of WAXS, EXAFS and XANES to compare structural data with the MD predictions. The predicted WAXS patterns give excellent agreement with data, while the predicted EXAFS and XANES spectra give poor agreement. Relative to WAXS, XANES and EXAFS spectra contain additional structural information related to the distribution of disorder. The discrepancy between the x-ray diffraction and x-ray absorption results indicates that structural disorder is partitioned between interior and surface regions more strongly than predicted in the MD simulations.     

On the solvation of the Zn2+ ion in methanol: a combined quantum mechanics, molecular dynamics, and EXAFS approach

The solvation properties of the Zn(2+) ion in methanol solution have been investigated using a combined approach based on molecular dynamics (MD) simulations and extended X-ray absorption fine structure (EXAFS) experimental results. The quantum mechanical potential energy surface for the interaction of the Zn(2+) ion with a methanol molecule has been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective Zn-methanol interactions have been fitted by suitable analytical potentials, and have been utilized in the MD simulation to obtain the structural properties of the solution. The reliability of the whole procedure has been assessed by comparing the theoretical structural results with the EXAFS experimental data. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to the EXAFS experiments.     

Glycosidic linkage conformation of methyl-alpha-mannopyranoside

We study the preferred conformation of the glycosidic linkage of methyl-alpha-mannopyranoside in the gas phase and in aqueous solution. Results obtained utilizing Car-Parrinello molecular dynamics (CPMD) simulations are compared to those obtained from classical molecular dynamics (MD) simulations. We describe classical simulations performed with various water potential functions to study the impact of the chosen water potential on the predicted conformational preference of the glycosidic linkage of the carbohydrate in aqueous solution. In agreement with our recent studies, we find that results obtained with CPMD simulations differ from those obtained from classical simulations. In particular, this study shows that the trans (t) orientation of the glycosidic linkage of methyl-alpha-mannopyranoside is preferred over its gauche anticlockwise (g-) orientation in aqueous solution. CPMD simulations indicate that this preference is due to intermolecular hydrogen bonding with surrounding water molecules, whereas no such information could be demonstrated by classical MD simulations. This study emphasizes the importance of ab initio MD simulations for studying the structural properties of carbohydrates in aqueous solution.     

Preferred conformation of the glycosidic linkage of methyl-beta-mannose

The conformational preference of the glycosidic linkage of methyl-beta-mannose was studied in the gas phase and in aqueous solution by ab initio calculations, and by molecular dynamics (MD) and Car-Parrinello molecular dynamics (CPMD) simulations. MD simulations were performed with various water potential functions to study the impact of the chosen water potential on the predicted conformational preference of the glycosidic linkage of the carbohydrate in solution. This study shows that the trans (t) orientation of the glycosidic linkage of methyl-beta-mannose is preferred over its gauche clockwise (g+) orientation in solution. CPMD simulations clearly indicate that this preference is due to intermolecular hydrogen bonding with surrounding water molecules, whereas no such information could be demonstrated by MD simulations. This study demonstrates the importance of ab initio molecular dynamics simulations in studying the structural properties of carbohydrate-water interactions.     

Hydrogen and higher shell contributions in Zn2+, Ni2+, and Co2+ aqueous solutions: an X-ray absorption fine structure and molecular dynamics study

A detailed investigation of the hydration structure of Zn2+, Ni2+, and Co2+ in water solutions has been carried out combining X-ray absorption fine structure (EXAFS) spectroscopy and Molecular Dynamics (MD) simulations. The first quantitative analysis of EXAFS from hydrogen atoms in 3d transition metal ions in aqueous solutions has been carried out and the ion-hydrogen interactions have been found to provide a detectable contribution to the EXAFS spectra. An accurate determination of the structural parameters associated with the first hydration shell has been performed and compared with previous experimental results. No evidence of significant contributions from the second hydration shell to the EXAFS signal has been found for these solutions, while the inclusion of the hydrogen signal has been found to be important in performing a quantitative analysis of the experimental data. The high-frequency contribution present in the EXAFS spectra has been found to be due to multiple scattering (MS) effects inside the ion-oxygen first coordination shell. MD has been used to generate three-body distribution functions from which a reliable analysis of the MS contributions to the EXAFS spectra of these systems has been carried out.     

Force field‐dependent solution properties of glycine oligomers

Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly₃ and Gly₁₀ in aqueous solution from all atom, microsecond molecular dynamics (MD) simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly₃ and Gly₁₀ were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g., end‐to‐end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. © 2015 Wiley Periodicals, Inc.     

Different Behaviors of ACE Inhibitor Tripeptide Ile-Ile-Pro in Aqueous and DMSO Solutions by All-Atom MD Simulations and 2D-NOESY Spectra

All-atom molecular dynamic simulations and 2D-NOESY spectra were used to study the conformations and hydrogen bonds of ACE inhibitory tripeptide Ile-Ile-Pro(IIP) in aqueous and DMSO solutions. RMSD, Dis, Rg and SASA were adopted to characterize the properties of tripeptide Ile-Ile-Pro in the MD simulations. Interestingly, the tripeptide molecule IIP exhibited different behaviors in aqueous and DMSO solutions. In aqueous solution, IIP was very flexible. The conformation could shift between extended and folded states very quickly. However,in DMSO solution, more folded conformations were observed. The interesting phenomena were proved by 2D-NOESY spectra.     

Importance of multiple-scattering phenomena in XAS structural determinations of [Ni(CN)4]2- in condensed phases

A quantitative analysis of the XAS spectra of the tetracyanonickelate complex [Ni(CN)4]2- has been carried out. The simultaneous study of the EXAFS and XANES regions yielded complementary information regarding the geometric and electronic structures of the complex. XANES spectra were modeled by applying recently developed self-consistent, full multiple-scattering algorithms in the FEFF8 code (version 8 x 34). XANES spectra for clusters of different sizes (from 9 to 125 atoms) were computed and compared with experimental spectra. This region of the spectra was proportional to a broadened Ni p-density of states diagram above the Fermi level. Although the main features of the XANES spectra were reasonably reproduced by computations, the weak dependence of the theoretical spectra on cluster size contrasts with the close similarity between the experimental spectra of the solid and solution systems. Because of the special geometry of the complex, calculations with polarized light parallel and perpendicular to the molecular plane were carried out, yielding a reasonable reproduction of the experimental data from another report for cluster sizes equal to or higher than 45 atoms. The highly symmetric square planar structure of the complex was found to be responsible for the unusual amplitude of the multiple-scattering (MS) contributions to the EXAFS spectra. Spectra in this region were fitted using the FEFFIT EXAFS analysis program, taking into account only the MS paths that simultaneously have both a high amplitude, as calculated with the ab initio code FEFF, and a small Debye-Waller factor, as estimated by the independent-vibration approximation model. Fitting results yielded very similar structures for the Ni2+ complex in the solid state and in solution, though the larger Debye-Waller factors found for the solid suggest higher static disorder in this state.     

Theoretical Study on Co^3＋ in Aqueous Solution in Terms of ABEEM/MM Model

A detailed theoretical investigation on Co^3＋ hydration in aqueous solution has been carded out by means of molecular dynamics （MD） simulations based on the atom-bond electronegativity equalization method fused into molecular mechanics （ABEEM/MM）. The effective Co^3＋ ion-water potential has been constructed by fitting to ab initio structures and binding energies for ionic clusters. And then the ion-water interaction potential was applied in combination with the ABEEM-7P water model to molecular dynamics simulations of single Co^3＋（aq.） solution, managing to reproduce many experimental structural and dynamical properties of the solution. Here, not only the common properties （radial distribution function, angular distribution function and solvation energy） obtained for Co^3＋ in ABEEM-7P water solution were in good agreement with those from the experimental methods and other molecular dynamics simulations but also very interesting properties of charge distributions, geometries of water molecules, hydrogen bond, diffusion coefficients, vibrational spectra are investigated by ABEEM/MM model.     

Computational evidence for a variable first shell coordination of the cadmium(II) ion in aqueous solution

In this paper, we present a state-of-the-art 100 ns molecular dynamics simulation of a cadmium(II) aqueous solution that highlights a very flexible ion first coordination shell which transits between hexa- and heptahydrated complexes. From this investigation, a dynamical picture of the water exchange process emerges that takes place through an associative mechanism for the solvent substitution reaction. Our procedure starts from the generation of an effective two-body potential from quantum mechanical ab initio calculations in which the many-body ion-water terms are accounted for by the polarizable continuum method (PCM). This approach is computationally very efficient and has allowed us to carry out extremely long molecular dynamics simulations, indispensable to reproduce the dynamic properties of the cadmium(II) aqueous solution. Quantum mechanical ab initio calculations of the hexa- and heptahydrated complexes extracted from MD configurations have revealed stable minima for both clusters with the water molecules arranged in T(h)() and C(2) symmetries in the hexa- and heptahydrated complexes, respectively, with a slight energetic preference for the heptahydrated one. Finally, a comparison of the calculated hexa- and heptahydrated cluster IR and Raman spectra with the experimental data in the literature, has demonstrated that the IR spectroscopy is not able to distinguish between the two species, whereas the Raman spectrum of the Cd(2+)-(H(2)O)(7) cluster provides a better agreement with the experimental data.     

Revised ionic radii of lanthanoid(III) ions in aqueous solution

A new set of ionic radii in aqueous solution has been derived for lanthanoid(III) cations starting from a very accurate experimental determination of the ion-water distances obtained from extended X-ray absorption fine structure (EXAFS) data. At variance with previous results, a very regular trend has been obtained, as expected for this series of elements. A general procedure to compute ionic radii in solution by combining the EXAFS technique and molecular dynamics (MD) structural data has been developed. This method can be applied to other ions allowing one to determine ionic radii in solution with an accuracy comparable to that of the Shannon crystal ionic radii.     

Structural and dynamic properties of concentrated alkali halide solutions: a molecular dynamics simulation study

The physicochemical properties of alkali halide solutions have long been attributed to the collective interactions between ions and water molecules in the solution, yet the structure of water in these systems and its effect on the equilibrium and dynamic properties of these systems are not clearly understood. Here, we present a systematic view of water structure in concentrated alkali halide solutions using molecular dynamics simulations. The results of the simulations show that the size of univalent ions in the solution has a significant effect on the dynamics of ions and other transport properties such as the viscosity that are correlated with the structural properties of water in aqueous ionic solution. Small cations (e.g., Li+) form electrostatically stabilized hydrophilic hydration shells that are different from the hydration shells of large ions (e.g., Cs+) which behave more like neutral hydrophobic particles, encapsulated by hydrogen-bonded hydration cages. The properties of solutions with different types of ion solvation change in different ways as the ion concentration increases. Examples of this are the diffusion coefficients of the ions and the viscosities of solutions. In this paper we use molecular dynamics (MD) simulations to study the changes in the equilibrium and transport properties of LiCl, RbCl, and CsI solutions at concentrations from 0.22 to 3.97 M.