A quantum mechanics, molecular dynamics and EXAFS investigation into the Hg2+ ion solvation properties in methanol solution

The coordination properties of the Hg2+ ion in methanol solution have been investigated by combining extended X-ray absorption fine structure (EXAFS) spectroscopy and Quantum Mechanics/Molecular Dynamics (QM/MD) calculations. An effective Hg-methanol two-body potential has been generated from QM calculations in which the effect of bulk solvent is accounted for by the polarizable continuum model (PCM). This effective potential is then used in the MD simulation to obtain the structural and dynamic properties of the solution, and the reliability of the entire procedure is assessed by comparing the theoretical structural results with the EXAFS experimental data. The outstanding outcome of this work is that the Hg2+ ion forms a stable sevenfold complex in methanol solution, where the first shell solvent molecules are arranged in a distorted pentagonal bipyramid geometry. In this geometry five methanol molecules are not located on the equatorial plane, but are displaced above and below the plane, forming a "crown" around the ion. The Hg2+ first coordination shell has been found to be very flexible, and several transitions among coordination numbers of 7, 8 and 6 are observed during the simulation

Unraveling the Sc3+ hydration geometry: the strange case of the far-coordinated water molecule

The hydration structure and dynamics of Sc3+ in aqueous solution have been investigated using a combined approach based on quantum mechanical (QM) calculations, molecular dynamics (MD) simulations, and extended X-ray absorption fine structure (EXAFS) spectroscopy. An effective Sc−water two-body potential has been generated from QM calculations and then used in the MD simulation of Sc3+ in water, and the reliability of the entire procedure has been assessed by comparing the theoretical structural results with the EXAFS experimental data. The outstanding outcome of this work is that the Sc3+ ion forms a well-defined capped square antiprism (SAP) complex in aqueous solution, where the eight water molecules closest to the ion are located at the vertexes of a SAP polyhedron, while the ninth water molecule occupying the capping position is unusually found at a very long distance from the ion. This far-coordinated water molecule possesses a degree of structure comparable with the other first shell molecules surrounding the ion at much shorter distances, and its presence gave us the unique opportunity to easily identify the geometry of the Sc3+ coordination polyhedron. Despite very strong ion−water interactions, the Sc3+ hydration shell is very labile, as the far-coordinated ligand allows first shell water molecules to easily exchange their positions both inside the solvation shell and with the rest of the solvent molecules

Unraveling the perturbation induced by Zn2+ and Hg2+ ions on the hydrogen bond patterns of liquid methanol

The perturbation induced by the Zn2+ and Hg2+ ions on the methanol hydrogen bond patterns has been investigated by means of Molecular dynamics simulations. The methanol structure in the ion second coordination shell has been found to be significantly altered by the presence of both ions, the structuring ability being larger for Zn2+. Remarkable modifications of the hydrogen bond structure and dynamics have been evidenced, and peculiar networks of hydrogen bonds have been highlighted where the methanol molecules act as a bridge between the ion first shell complex and the bulk solvent. © 2015 Elsevier B.V. All rights reserved

Deep eutectic solvents: A structural point of view on the role of the anion

The structural properties of four deep eutectic solvents (DESs), namely a 1:2 mixture of choline chloride and urea, and three analogous DESs containing different anions in place of chloride, namely fluoride, nitrate or acetate, were investigated by using Molecular Dynamics. The order of the DES melting points was found not to correlate with the strength of urea-anion hydrogen bonds. However, the DES low melting points are related to the anion ability to build favourable networks of interactions with both choline and urea, in such a way as to maximize the hydrogen bonds among all the different moieties of the system

Solvation structure of Zn2+ and Cu2+ ions in acetonitrile: a combined EXAFS and XANES study

The solvation structure of Zn2+ and Cu2+ in acetonitrile has been determined by a combined approach using both X-ray absorption near edge structure (XANES) and the extended X-ray absorption fine structure (EXAFS) spectroscopy. For the former cation, an octahedral geometry of the acetonitrile solvate complex has been found with a Zn-N distance of 2.12(1) Å. For the Cu2+ solvates the EXAFS technique has been found to be not able to provide a conclusive determination of the coordination numbers and polyhedral environment, while the analysis of the XANES spectra unambiguously shows the existence of an axially elongated square pyramidal coordination, ruling out the previously proposed octahedral Jahn-Teller (JT) distorted geometry. The Cu-N distances obtained are 2.00(1) and 2.28(2) Å for the equatorial and axial ligands, respectively, and the EXAFS and XANES techniques find values of the bond distances in good agreement. The XANES technique has proven to be extremely powerful in providing a reliable resolution of solution structure for dynamic ion complexes. © 2015 American Chemical Society

Combined distribution functions: a powerful tool to identify cation coordination geometries in liquid systems

In this work we have developed an analytical procedure to identify metal ion coordination geometries in liquid media based on the calculation of Combined Distribution Functions (CDFs) starting from Molecular Dynamics (MD) simulations. CDFs provide a fingerprint which can be easily and unambiguously assigned to a reference polyhedron. The CDF analysis has been tested on five systems and has proven to reliably identify the correct geometries of several ion coordination complexes. This tool is simple and general and can be efficiently applied to different MD simulations of liquid systems. © 2017 Elsevier B.V