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A novel model of hydration for the chloride and iodide ions in water is proposed, which overcomes the limitations of conventional radial models. A new approach, based on a representation of the halide lone pairs, highlighted a subset of first shell water molecules featuring preferential strong interactions with the ion lone pairs, giving rise to tetrahedral hydration structures in both Cl - and I - aqueous solutions. By adopting a novel descriptor correlated to the halide-water interaction energy, we were able to split the conventional first solvation shell into a tight first hydration shell, composed of water molecules strongly interacting with the ions via hydrogen bonds, and a loose first shell containing molecules that are only slightly perturbed by the halide electrostatic charge. The picture emerging from our findings indicates that lone pairs play an important role in the description of systems where hydrogen bonds are the main interactions taking place in the solvation process.

An approach combining molecular dynamics (MD) simulations and X-ray absorption spectroscopy (XAS) has been used to carry out a comparative study about the solvation properties of dilute La(NO 3 ) 3 solutions in water and methanol, with the aim of elucidating the still elusive coordination of the La 3+ ion in the latter medium. The comparison between these two systems enlightened a different behavior of the nitrate counterions in the two environments: while in water the La(NO 3 ) 3 salt is fully dissociated and the La 3+ ion is coordinated by water molecules only, the nitrate anions are able to enter the metal first solvation shell to form inner-sphere complexes in methanol solution. The speciation of the formed complexes showed that the 10-fold coordination is preferential in methanol solution, where the nitrate anions coordinate the La 3+ cations in a monodentate fashion and the methanol molecules complete the solvation shell to form an overall bicapped square antiprism geometry. This is at variance with the aqueous solution where a more balanced situation is observed between the 9- and 10-fold coordination. An experimental confirmation of the MD results was obtained by La K-edge XAS measurements carried out on 0.1 M La(NO 3 ) 3 solutions in the two solvents, showing the distinct presence of the nitrate counterions in the La 3+ ion first solvation sphere of the methanol solution. The analysis of the extended X-ray absorption fine structure (EXAFS) part of the absorption spectrum collected on the methanol solution was carried out starting from the MD results and confirmed the structural arrangement observed by the simulations.

The changes upon methanol (MeOH) addition in the structural arrangement of the highly eco-friendly deep eutectic solvent (DES) formed by choline chloride (ChCl) and sesamol in 1:3 molar ratio have been studied by means of attenuated total reflection Fourier transform infrared spectroscopy, small- and wide-angle X-ray scattering (SWAXS), and molecular dynamics simulations. The introduction of MeOH into the DES promotes the increase of the number of Cl-MeOH hydrogen bonds (HBs) through the replacement of sesamol and choline molecules from the chloride anion coordination sphere. This effect does not promote the sesamol-sesamol, choline-choline, and sesamol-choline interactions, which remain as negligible as in the pure DES. Differently, the displaced sesamol and choline molecules are solvated by MeOH, which also forms HBs with other MeOH molecules, so that the system arranges itself to keep the overall amount of HBs maximized. SWAXS measurements show that this mechanism is predominant up to MeOH/DES molar ratios of 20-24, while after this ratio value, the scattering profile is progressively diluted in the cosolvent background and decreases toward the signal of pure MeOH. The ability of MeOH to interplay with all of the DES components produces mixtures with neither segregation of the components at nanoscale lengths nor macroscopic phase separation even for high MeOH contents. These findings have important implications for application purposes since the understanding of the pseudophase aggregates formed by a DES with a dispersing cosolvent can help in addressing an efficient extraction procedure., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)

A thorough structural characterization of the La(NO 3 ) 3 salt dissolved into several mixtures of ethyl ammonium nitrate (EAN) and methanol (MeOH) with EAN molar fraction χ EAN ranging from 0 to 1 has been carried out by combining molecular dynamics (MD) and X-ray absorption spectroscopy (XAS). The XAS and MD results show that changes take place in the La 3+ first solvation shell when moving from pure MeOH to pure EAN. With increasing the ionic liquid content of the mixture, the La 3+ first-shell complex progressively loses MeOH molecules to accommodate more and more nitrate anions. Except in pure EAN, the La 3+ ion is always able to coordinate both MeOH and nitrate anions, with a ratio between the two ligands that changes continuously in the entire concentration range. When moving from pure MeOH to pure EAN, the La 3+ first solvation shell passes from a 10-fold bicapped square antiprism geometry where all the nitrate anions act only as monodentate ligands to a 12-coordinated icosahedral structure in pure EAN where the nitrate anions bind the La 3+ cation both in mono- and bidentate modes. The La 3+ solvation structure formed in the MeOH/EAN mixtures shows a great adaptability to changes in the composition, allowing the system to reach the ideal compromise among all of the different interactions that take place into it.

The structural properties of the deep eutectic solvent (DES) formed by choline chloride (ChCl) and sesamol in 1 : 3 ratio have been investigated and compared to those of reline (ChCl : urea 1 : 2). An integrated approach combining small and wide angle X-ray scattering with molecular dynamics simulations has been employed and the simulation protocol has been validated against the experimental data. In the ChCl : sesamol DES, strong hydrogen bonds (HBs) are formed between the chloride anion and the hydroxyl groups of the choline and of sesamol molecules. Conversely, choline-choline, choline-sesamol and sesamol-sesamol interactions are negligible. A more extended interplay between the constituents is observed in reline where, besides the HBs involving the chloride anion, the eutectic formation is favored also by strong choline-urea and urea-urea interactions. The three-dimensional arrangement around the individual components shows that, in the ChCl : sesamol DES, the cholinium cations and the sesamol molecules are packed in such a way to maximize the interactions with the chlorine anion. This structural arrangement may favor the π-π interactions between the sesamol molecules and the aromatic species mediated by the chloride ions, providing an interpretation for the high separation rates previously observed for phenolic DESs towards aromatic compounds.

X-ray absorption spectroscopy (XAS) has been employed to study the coordination of the Ag + ion in aqueous solution. The conjunction of extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) data analysis provided results suggesting the preference for a first shell linear coordination with a mean Ag-O bond distance of 2.34(2) Å, different from the first generally accepted tetrahedral model with a longer mean Ag-O bond distance. Ab initio molecular dynamics simulations with the Car-Parrinello approach (CPMD) were also performed and were able to describe the coordination of the hydrated Ag + ion in aqueous solution in very good agreement with the experimental data. The high sensitivity for the closest environment of the photoabsorber of the EXAFS and XANES techniques, together with the long-range information provided by CPMD and large-angle X-ray scattering (LAXS), allowed us to reconstruct the three-dimensional model of the coordination geometry around the Ag + ion in aqueous solution. The obtained results from experiments and theoretical simulations provided a complex picture with a certain amount of water molecules with high configurational disorder at distances comprised between the first and second hydration spheres. This evidence may have caused the proliferation of the coordination numbers that have been proposed so far for Ag + in water. Altogether these data show how the description of the hydration of the Ag + ion in aqueous solution can be complex, differently from other metal species where hydration structures can be described by clusters with well-defined geometries. This diffuse hydration shell causes the Ag-O bond distance in the linear [Ag(H 2 O) 2 ] + ion to be ca. 0.2 Å longer than in isolated ions in solid state.

A synergic approach combining molecular dynamics (MD) and X-ray absorption spectroscopy (XAS) has been used to investigate the structural properties of the La(Tf2N)3 salt (where Tf2N = bistriflimide or bis(trifluoromethansulfonyl)imide) dissolved into several mixtures of acetonitrile and the 1,8-bis(3-methylimidazolium-1-yl)octane bistriflimide (C8(mim)2(Tf2N)2) ionic liquid (IL), with the IL molar fraction (χIL) ranging from 0 to 1. The XAS and MD results show that major changes take place in the La3+ first solvation shell when moving from pure acetonitrile to pure C8(mim)2(Tf2N)2. With increasing the IL concentration of the mixture, the La3+ first shell complex progressively loses acetonitrile molecules to accommodate more and more oxygen atoms of the Tf2N- anions. Except in pure C8(mim)2(Tf2N)2, La3+ is always able to coordinate both acetonitrile and Tf2N- anions, with a ratio between the two different ligands strongly dependent on the IL content. Moreover, the La3+ ion prefers to form a 10-coordinated first shell complex in all the investigated systems, with a slightly different geometry of the cluster depending on the composition of the La3+ first solvation shell. In particular, when moving from pure acetonitrile to pure C8(mim)2(Tf2N)2, the La3+ first solvation shell passes from a bicapped square antiprism geometry where all the Tf2N- anions act only as monodentate ligands, to a "1 + 5 + 4" structure in which the Tf2N- anion binds La3+ both in a monodentate and bidentate fashion. The great adaptability shown by the La3+ solvation structure allows it to reach the optimal balance among many different forces at play involving all of the different species present in the mixtures.

The structural and dynamic properties of the Ba 2+ cation in water have been studied by combining quantum mechanical (QM) calculations, molecular dynamics (MD) simulations, and extended X-ray absorption fine structure (EXAFS) spectroscopy. An effective Ba 2+ -water interaction potential, to be used in the MD simulation of a Ba 2+ aqueous solution, has been developed by means of QM methods, and the validity of the whole procedure has been assessed by comparing the theoretical structural results with the EXAFS experimental data. By combining distance and angular distribution functions it was possible to unambiguously identify the geometry adopted by the water molecules surrounding the ion in the solution. The Ba 2+ ion was found to preferentially form an 8-fold first shell complex with a bicapped trigonal prism (BTP) geometry. The 8-fold complex is in equilibrium with a 9-fold structure having a tricapped trigonal prism (TTP) geometry, and the hydration shell is very diffuse and flexible, being characterized by a very fast solvent exchange process on the picosecond time scale.

A synergic approach combining molecular dynamics (MD) and extended X-ray absorption fine structure (EXAFS) spectroscopy has been used to investigate weak-concentrated (0.1 M) acetonitrile solutions of La(Tf 2 N) 3 and Dy(Tf 2 N) 3 salts (where Tf 2 N is the bis(trifluoromethanesulfonyl)imide). The MD simulations show that contact ion pairs between the Ln 3+ cations and the Tf 2 N - anions are formed in the solutions. This finding has been experimentally confirmed by the analysis of the Ln K-edge EXAFS experimental signals of the two solutions. Both La 3+ and Dy 3+ ions preferentially form a 10-fold first shell complex composed of acetonitrile molecules and Tf 2 N - counterions with a bicapped square antisprism (BSAP) geometry. As a consequence of lanthanide contraction, the Dy 3+ cation binds the inner shell solvent molecules at shorter distances as compared to La 3+ and the high charge density of Dy 3+ allows the coordination with additional ligands at longer distances. On the other hand, the bigger La 3+ ion forms a very crowded coordination shell with a larger average distance and with the capped molecules at distances from the ion more similar to the inner shell ones. This peculiar coordination structure could explain the high catalytic activity of the Ln-Tf 2 N complexes and the high Lewis acidity of the lanthanide center.

A synergic approach combining molecular dynamics (MD) simulations and X-ray absorption spectroscopy (XAS) has been used to investigate diluted (0.1 M) aqueous solutions of two lanthanide ions (Ln 3+ ), namely, La 3+ and Dy 3+ , with triflate, nitrate, and bis(trifluoromethylsulfonyl)imide (Tf 2 N - ) as counterions. The different complexing ability of the three anions has been highlighted by the analysis of the MD simulations: Tf 2 N - does not form inner-sphere complexes, while a small amount of triflate coordinates both the La 3+ and Dy 3+ cations in their first solvation shell. On the other hand, the nitrate ion is almost absent in the La 3+ first coordination sphere, while forming contact ion pairs with Dy 3+ . Both lanthanide ions are found to preferentially interact with the water molecules, and the total number of oxygen atoms coordinating the Ln 3+ cations in their first solvation sphere is the same in all of the solutions, regardless of whether they belong to water molecules or to the counterion. The presence of counterions in the cation first or second shell changes neither the first shell distance nor the symmetry of the hydration complex formed in solution. The MD results have been confirmed by comparison with the Ln K-edge XAS experimental data, and the quantitative analysis of the extended X-ray absorption fine structure (EXAFS) spectra of the three salt solutions has provided a definite proof of the accuracy of the force field employed in the simulations and of the MD structural result. The anion-water and water-water hydrogen bond lifetimes have been analyzed highlighting the slow down effect of the triflate, nitrate, and Tf 2 N - anions on the hydrogen bond dynamics in the Ln 3+ first solvation shell, with the effect being stronger in the Dy 3+ solutions, due to the higher charge density of the Dy 3+ ion as compared to La 3+ .

A synergic approach combining molecular dynamics (MD) simulations and X-ray absorption spectroscopy has been used to investigate diluted solutions of zinc bis(trifluoromethanesulfonyl)imide (Zn(Tf 2 N) 2 ) in Tf 2 N - based ionic liquids (ILs) having different organic cations, namely the 1-butyl-3-methylimidazolium ([C 4 (mim)] + ), 1,8-bis(3-methylimidazolium-1-yl)octane ([C 8 (mim) 2 ] 2+ ), N,N,N-trimethyl-N-(2-hydroxyethyl)ammonium ([Choline] + ) and butyltrimethylammonium ([BTMA] + ) ions. All of the ILs tend to dissolve the Zn(Tf 2 N) 2 species giving rise to a different structural arrangement around the Zn 2+ as compared to that of the salt crystallographic structure. A quantitative analysis of the Zn K-edge extended X-ray absorption fine structure (EXAFS) spectra of the solutions has been carried out based on the microscopic description of the systems derived from the MD simulations. A very good agreement between theoretical and experimental EXAFS signals has been obtained, allowing us to assess the reliability of the MD structural results for all the investigated solutions. The Zn 2+ ion has been shown to be coordinated by six oxygen atoms of the Tf 2 N - anions arranged in an octahedral geometry in all the Tf 2 N - based ILs, regardless of the organic cation of the IL solvent. However, the nature of the organic cation has a small influence on the overall spatial arrangement of the Tf 2 N - anions in the Zn 2+ first solvation shell: two different Zn-Tf 2 N complexes are found in solution, a 5-fold one, with one bidentate and four monodentate Tf 2 N - anions, and a 6-fold one with only monodentate ligands, with the ratio between the two species being slightly dependent on the IL cation. The IL ion three-dimensional arrangements in the different IL solutions were also investigated by carrying out a thorough analysis of the MD simulations, highlighting similarities and differences between imidazolium and ammonium based IL systems.

The structural modifications induced on a 0.5 M Zn 2+ aqueous solution by increasing the pressure to 6.4 GPa were investigated using a combination of X-ray absorption near edge structure (XANES) spectroscopy and molecular dynamics (MD) simulations. The Zn K-edge XANES experimental spectra show two different trends depending on the pressure and temperature conditions of the system. On the one hand, when the pressure is increased to 1.0 GPa while keeping the temperature at 300 K, the highly structured nature of Zn 2+ second hydration shell is preserved. On the other hand, when the Zn 2+ aqueous solution is simultaneously pressurized and heated to follow the melting curve above 1.0 GPa, the Zn 2+ second shell loses its high degree of structuring and becomes much more disordered and unstructured. These results are confirmed by the analysis of MD simulations of Zn 2+ aqueous solutions under high pressure. By combining distance and angular distribution functions it is possible to highlight the loss of water structuring in the Zn 2+ second coordination shell that takes place upon pressurization and heating. A progressive crowding of the Zn 2+ second shell is observed with increasing pressure; the water structure becomes remarkably different from that found at ambient conditions, and for pressure values higher than 1.0 GPa the tetrahedral arrangements of water molecules is highly distorted. Moreover, MD simulations of Zn 2+ aqueous solutions performed at 1.0 GPa and at increasing temperature values have shown that the loss of water structuring in the Zn 2+ second coordination shell observed by simultaneously pressurizing and heating is due to a combined effect of pressure and temperature, both producing an increase of the Zn 2+ second-shell disorder.

In this contribution, we show how it is possible to develop polarizable and non-polarizable force fields to study hydration properties of a whole chemical series based on atomic properties such as ionic radii. In particular, we have addressed the actinide(III) ion series, from U 3+ to Cf 3+ , for which X-ray absorption data and effective ionic radii are available. A polarizable force field has been re-parameterized improving the original one [M. Duvail et al., J. Chem. Phys. 135, 044503 (2011)] which was based on solid state ionic radii. The new force field does not depend on solid state properties but directly on the liquid phase ones, and it can be used to study these ions in liquid water without any ambiguity. Furthermore, we have shown that it is possible to parameterize also a non-polarizable potential using standard Lennard-Jones and Coulombic forces, which can be transferred to other systems in condensed phase. The structural and dynamical properties of these two force fields are compared to each other and with data available in the literature, providing a good agreement. Moreover, we show the comparison with experimental X-ray absorption data that are very well reproduced by both force fields.

An innovative approach aimed at disclosing the mechanism of chemical reactions occurring in solution on the millisecond time scale is presented. Time-resolved energy dispersive X-ray absorption and UV/vis spectroscopies with millisecond resolution are used simultaneously to directly follow the evolution of both the oxidation state and the local structure of the metal center in an iron complex. Two redox reactions are studied, the former involving the transformation of Fe II into two subsequent Fe III species and the latter involving the more complex Fe II -Fe III -Fe IV -Fe III sequence. The structural modifications occurring around the iron center are correlated to the reaction mechanisms. This combined approach has the potential to provide unique insights into reaction mechanisms in the liquid phase and represents a new powerful tool to characterize short-lived intermediates that are silent to common spectroscopic techniques.

A diluted solution of Ce(NO 3 ) 3 in the protic ionic liquid (IL) ethylammonium nitrate (EAN) was investigated using molecular dynamics (MD) simulations and extended X-ray absorption fine structure (EXAFS) spectroscopy. For the first time polarizable effects were included in the MD force field to describe a heavy metal ion in a protic IL, but, unlike water, they were found to be unessential. The Ce III ion first solvation shell is formed by nitrate ions arranged in an icosahedral structure, and an equilibrium between monodentate and bidentate ligands is present in the solution. By combining distance and angular distribution functions it was possible to unambiguously identify this peculiar coordination geometry around the ions dissolved in solution. The metal ions are solvated within the polar domains of the EAN nanostructure and the dissolved salt induces almost no reorganization of the pre-existing structure of EAN upon solubilization., (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

New sets of Lennard-Jones and Buckingham potentials have been developed to be used in classical molecular dynamics simulations of Ln 3+ -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 Ln 3+ -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 Ln 3+ 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 Ln 3+ 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 Ln 3+ ions in different disordered systems.

The hydration structure and dynamics of Sc(3+) 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 Sc(3+) 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 Sc(3+) 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 Sc(3+) coordination polyhedron. Despite very strong ion-water interactions, the Sc(3+) 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.

The structural behavior of geminal dicationic ionic liquid 1,n-bis[3-methylimidazolium-1-yl] alkane bromide ([Cn(mim)2]Br2)/water mixtures has been studied using extended X-ray absorption fine structure (EXAFS) spectroscopy in combination with molecular dynamics (MD) simulations. The properties of the mixtures are investigated as a function of both water concentration and alkyl-bridge chain length. The very good agreement between the EXAFS experimental data and the theoretical curves calculated from the MD structural results has proven the validity of the theoretical framework used for all of the investigated systems. In all the solutions the water molecules are preferentially coordinated with the Br(-) ion, even if a complex network of interactions among dications, anions and water molecules takes place. The local molecular arrangement around the bromide ion is found to change with increasing water content, as more and more water molecules are accomodated in the Br(-) first coordination shell. Moreover, with the decrease of the alkyl-bridge chain length, the interactions between dications and anions increase, with Br(-) forming a bridge between the two imidazolium rings of the same dication. On the other hand, in [Cn(mim)2]Br2/water mixtures with long alkyl-bridge chains peculiar internal arrangements of the dications are found, leading to different structural features of geminal dicationic ionic liquids as compared to their monocationic counterparts.

X-ray absorption near-edge structure (XANES) spectroscopy has been used to determine the structure of the hydrated strontium in aqueous solution. The XANES analysis has been carried out using solid [Sr(H2O)8](OH)2 as reference model. Classical and Car-Parrinello molecular dynamics (MD) simulations have been carried out and in the former case two different sets of Lennard-Jones parameters have been used for the Sr(2+) ion. The best performing theoretical approach has been chosen on the basis of the experimental results. XANES spectra have been calculated starting from MD trajectories, without carrying out any minimization of the structural parameters. This procedure allowed us to properly account for thermal and structural fluctuations occurring in the aqueous solution in the analysis of the experimental spectrum. A deconvolution procedure has been applied to the raw absorption data thus increasing the sensitivity of XANES spectroscopy. One of the classical MD simulations has been found to provide a XANES theoretical spectrum in better agreement with the experimental data. An 8-fold hydration complex with a Sr-O distance of 2.60 Å has been found to be compatible with the XANES data, in agreement with previous findings. However, the hydration shells of the strontium ions have been found to have a flexible nature with a fast ligand exchange rate between the first and second hydration shell occurring in the picosecond time scale.

An elusive tetrahedral hydration structure for bromide in aqueous solution has been unveiled through the use of ab initio molecular dynamics. It has been revealed that a subset of first shell water molecules has a preferential strong interaction with the ion lone pairs, giving rise to a tetrahedral short-lived complex. Through the use of a new geometric descriptor correlated to the ion-water pair interaction energy, we managed to divide the conventional first hydration shell into a tight first shell and a loose first shell, highlighting their different structural and dynamic behavior. This picture suggests the mandatory role of lone pairs in the study of highly disordered systems where the hydrogen bond is the most relevant interaction in the solvation process, such as weakly hydrated anions. This interaction-based approach leads to an improvement in the description of halide hydration given up to now by radial models.

The structural properties of 1-hexyl-3-methylimidazolium iodide ([C6mim]I)/water mixtures with molar ratios ranging from 1:1 to 1:200 have been investigated using molecular dynamics (MD) simulations with extended X-ray absorption fine structure (EXAFS) experimental data. The presence of a complex network of interactions among cations, anions, and water molecules has been highlighted from the MD simulations, even if water molecules have been found to interact preferentially with the I(-) anion. The EXAFS results show that, also for the 1:1 [C6mim]I/water mixture, the water molecules are placed next to the I(-) anion, and the I(-) hydration shell becomes more and more crowded with increasing water content. Tight ion pairs have been detected in the [C6mim]I/water mixtures with molar ratios from 1:1 to 1:12, while no ionic pairs were found in the most diluted solutions. The aggregation behavior has been determined from MD simulations with the aid of S(q) functions. For the most concentrated IL/water mixtures with molar ratios between 1:1 and 1:12 the existence of long-range structural correlations has been evidenced, even if the apolar chains are not completely segregated as expected for micelle-like structures. Conversely, for the 1:200 mixture, that is above the experimental critical aggregation concentration value, the alkyl chains are completely separated from each other.

The conversion of the prion protein (PrP(C)) into prions plays a key role in transmissible spongiform encephalopathies. Despite the importance for pathogenesis, the mechanism of prion formation has escaped detailed characterization due to the insoluble nature of prions. PrP(C) interacts with copper through octarepeat and non-octarepeat binding sites. Copper coordination to the non-octarepeat region has garnered interest due to the possibility that this interaction may impact prion conversion. We used X-ray absorption spectroscopy to study copper coordination at pH 5.5 and 7.0 in human PrP(C) constructs, either wild-type (WT) or carrying pathological mutations. We show that mutations and pH cause modifications of copper coordination in the non-octarepeat region. In the WT at pH 5.5, copper is anchored to His96 and His111, while at pH 7 it is coordinated by His111. Pathological point mutations alter the copper coordination at acidic conditions where the metal is anchored to His111. By using in vitro approaches, cell-based and computational techniques, we propose a model whereby PrP(C) coordinating copper with one His in the non-octarepeat region converts to prions at acidic condition. Thus, the non-octarepeat region may act as the long-sought-after prion switch, critical for disease onset and propagation.

A thorough characterization of the structural properties of alkylimidazolium halide ionic liquids (ILs), namely 1-alkyl-3-methylimidazolium bromide ([Cnmim]Br with n = 5, 6, 8, 10) and iodide ([C6mim]I), has been carried out by combining molecular dynamics simulations and EXAFS spectroscopy. The existence of a local order in [Cnmim]Br ILs has been evidenced, with anions and imidazolium head groups forming a local three-dimensional bonding pattern that is common to all the [Cnmim]Br IL family, regardless of the length of the alkyl chain attached to the cation. On the other hand, upon alkyl chain elongation significant differences have been highlighted in the long-range structure of these ILs. Theoretical X-ray structure factors have been calculated from MD simulations and a low q peak has been found for all [Cnmim]Br ILs, indicating the existence of long-range structural correlations. The low q peak moves to smaller q values corresponding to longer distances, increases in intensity and sharpens with increasing alkyl chain length on the cation. Similarities and differences between the ion three-dimensional arrangements in [C6mim]Br and [C6mim]I were highlighted and the structural arrangement of Br(-) and I(-) was found to be different in the proximity of the most acidic hydrogen atom of the imidazolium ring: the I(-) ion is preferentially located above and below the ring plane, while the Br(-) ion has a high probability also to be coplanar with the imidazolium ring. A quantitative analysis of the Br and I K-edge EXAFS spectra of alkylimidazolium halide ILs has been carried out based on the microscopic description of the systems derived from MD simulations. A very good agreement between theoretical and experimental EXAFS signals has been obtained, allowing us to assess the reliability of the MD structural results for all the alkylimidazolium halide ILs investigated in this work.

The solvation structure of Zn(2+) and Cu(2+) 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 Cu(2+) 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.

The structural properties of liquid 1-butyl-3-methylimidazolium iodide [C4mim]I have been investigated using an integrated approach that combines EXAFS spectroscopy and molecular dynamics (MD) simulations. A well defined first coordination shell composed on average of 4.5 I(-) ions around the imidazolium cation has been evidenced, and the structural arrangement of the I(-) ions has been found to be different in the proximity of the most acidic hydrogen atom of the imidazolium ring, as compared to the other two ring protons: in the former case the I(-) ion is not coplanar with the imidazolium ring plane, but it prefers to be above and below the plane itself, while in the latter the anion has the same probability of being or not being coplanar with the plane. A quantitative analysis of the I K-edge EXAFS spectrum of liquid [C4mim]I has been carried out starting from the structural information on the system derived from the MD simulation. This combined approach allows one to reduce the number of correlated model parameters required in the fitting of the experimental data and to increase the reliability of the EXAFS data analysis that represents a non-trivial task when dealing with disordered systems. Moreover, the good agreement between the EXAFS experimental and theoretical spectra of liquid [C4mim]I has proven the reliability of the MD results and force field employed.

A deconvolution procedure has been applied to K-edge X-ray absorption near-edge structure (XANES) spectra of lanthanoid-containing solid systems, namely, hexakis(dmpu)praseodymium(III) and -gadolinium(III) iodide. The K-edges of lanthanoids cover the energy range 38 (La)-65 (Lu) keV, and the large widths of the core-hole states lead to broadening of spectral features, reducing the content of structural information that can be extracted from the raw X-ray absorption spectra. Here, we demonstrate that deconvolution procedures allow one to remove most of the instrumental and core-hole lifetime broadening in the K-edge XANES spectra of lanthanoid compounds, highlighting structural features that are lost in the raw data. We show that quantitative analysis of the deconvolved K-edge XANES spectra can be profitably used to gain a complete local structural characterization of lanthanoid-containing systems not only for the nearest neighbor atoms but also for higher-distance coordination shells.

The hydration properties of halide aqua ions have been investigated combining classical Molecular Dynamics (MD) with Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy. Three halide-water interaction potentials recently developed [M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)], along with three plausible choices for the value of the absolute hydration free energy of the proton (ΔG [minus sign in circle symbol]hyd[H+]), have been checked for their capability to properly describe the structural properties of halide aqueous solutions, by comparing the MD structural results with EXAFS experimental data. A very good agreement between theory and experiment has been obtained with one parameter set, namely LE, thus strengthening preliminary evidences for a ΔG [minus sign in circle symbol]hyd[H] value of -1100 kJ mol(-1) [M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)]. The Cl(-), Br(-), and I(-) ions have been found to form an unstructured and disordered first hydration shell in aqueous solution, with a broad distribution of instantaneous coordination numbers. Conversely, the F(-) ion shows more ordered and defined first solvation shell, with only two statistically relevant coordination geometries (six and sevenfold complexes). Our thorough investigation on the effect of halide ions on the microscopic structure of water highlights that the perturbation induced by the Cl(-), Br(-), and I(-) ions does not extend beyond the ion first hydration shell, and the structure of water in the F(-) second shell is also substantially unaffected by the ion.

The structural and dynamic properties of 1-butyl-3-methylimidazolium bromide ([C4mim]Br)/water mixtures with different molar ratios have been investigated using classical molecular dynamics (MD) simulations, and the reliability of the results has been assessed by comparison with extended X-ray absorption fine structure experimental data. The analysis of the MD trajectories has highlighted the presence of a complex network of interactions among cations, anions, and water molecules, even if water molecules have been found to interact preferentially with the Br(-) anion. The existence of solvent-shared ion pairs has been detected in all of the investigated mixtures with one or more water molecules acting as a bridge between the cation and the anion, also when water is present in great excess ([C4mim]Br/water ratio of 1:200). The dynamic behavior of the systems has been characterized starting from the MD trajectories. Water molecules have been found to quicken the dynamics of the IL cations and anions, and acceleration involves all of the investigated motions.

Extended X-ray absorption fine structure (EXAFS) spectroscopy is employed, in conjunction with molecular dynamics (MD) simulations, to investigate the interaction of water with the Br(-) ion in an imidazolium-based ionic liquid (IL). 1-Butyl-3-methylimidazolium bromide/water mixtures with molar ratios ranging from 1:3 to 1:200 have been analyzed, and a clear picture of the structural arrangements of the water molecules inside the IL has been obtained from the synergic interpretation of the EXAFS and MD data. At the lowest investigated water content, the presence of water is mainly detected around the Br(-) anion. Upon increasing the water fraction, more water molecules enter the Br(-) first-coordination shell but always in a lower number than what is needed to saturate the inner sphere. This suggests that interactions also exist between water and the imidazolium cation. The existence of tight ion pairs has been evidenced, even when water is present in the mixtures in great excess.

The analysis of the thermal behavior of octyl- (OAC) and decylammonium chloride (DAC) has provided relevant new information. OAC shows a polymorphic phase transition that starts at 308 K and is completed at 313 K, between a monoclinic and a tetragonal structure, which belongs to a space group different from what was observed for other alkylammonium chlorides. At the melting temperature (463 K), the growing of a strong first sharp diffraction peak (FSDP) occurring at a d-spacing of ca. 21.0 Å was observed. DAC is characterized by two phase transitions at 318 (T(d1)) and 323 K (T(d2)). At T(d1), the LT polymorph coexists with a new-formed phase. At T(d2) the LT polymorph is replaced by a further polymorphic modification of DAC that becomes the only one at 328 K. This second phase transition signals the occurrence of a phase, closely related to the LT polymorph of HeAC, that crystallizes in the tetragonal crystal system a = ca. 5.00 Å and c = ca. 28.5 Å, P4/nmm space group. DAC melting starts at 458 K and is accompanied, as in the case of OAC, by the growing of a strong FSDP at a d-spacing of ca. 24.8 Å. A parallel DSC study confirmed the above-mentioned transitions. In addition, the structural properties of OAC/water and DAC/water mixtures were studied using an integrated approach, which combines X-ray diffraction and molecular dynamics (MD) techniques. A very good agreement between theoretical and experimental diffraction patterns has been obtained for both investigated mixtures. A thorough analysis of the MD trajectories shows that strong anion-water interactions are present in the mixtures, where Cl(-) forms a rather unstructured first hydration shell of water molecules bound to the anion in a linear Cl···H-O configuration. Moreover, cations and anions were found to interact with each other, and to form "solvent-shared ion pairs", in which one or more water molecules are shared between Cl(-) and the alkylammonium cation.

The potential of high energy XANES (X-ray absorption near edge structure) as a tool for the structural analysis of lanthanoid-containing systems has been explored. The K-edge XANES spectra of La(3+), Gd(3+), and Lu(3+) ions both in DMSO solution and solid octakis(DMSO)lanthanoid(III) iodides have been analysed. Although the K-edges of lanthanoids cover the energy range of 38 (La) to 65 (Lu) keV, the large widths of the core hole states do not appreciably reduce the potential structural information of the XANES data. We show that, for lanthanoid compounds, accurate structural parameters are obtained from the analysis of K-edge XANES signals if a deconvolution procedure is carried out. We found that in solid octakis(DMSO)lanthanoid(III) iodides the Ln(3+) ions are coordinated by eight DMSO ligands arranged in a quite symmetric fashion. In DMSO solution the Ln(3+) ions retain a regular eight-coordination structure and the coordination number does not change along the series. In contrast to when in water the second coordination shell has been found to provide a negligible contribution to the XANES spectra of Ln(3+) ions in DMSO solution.

The structure and dynamics of water in ionic solutions at high pressure have been investigated using a combined approach based on extended X-ray absorption fine structure (EXAFS) spectroscopy and Molecular Dynamics (MD) simulations. Modification of the hydration properties of the Zn(2+) ion induced by a pressure increase from ambient condition up to ∼6.4 GPa has been revealed and accurately analyzed. With increasing pressure the first hydration shell of the Zn(2+) ion has been found to retain an octahedral symmetry with a shortening of the Zn-O distance up to 0.09 Å and an increased width associated with thermal motion, as compared to the ambient condition hydration complex. A very interesting picture of the dynamic behavior of the first hydration shell has emerged from the analysis of the simulations: up to 2.5 GPa no exchange events between first and second shell water molecules occurred, while above this pressure value several exchange events take place in the solution following an associative interchange mechanism. This result can be explained by the very high compression and packing of the solvent which force second shell water molecules to enter the Zn(2+) first hydration shell. MD simulations indicate a strong pressure effect also on the structure of the second coordination shell which is compressed and becomes more disordered and less structured with increasing pressure. The water mobility and the ion diffusion coefficient have been found to increase in the high density conditions, as a consequence of the rupture of the hydrogen bond network caused by pressure.

In this study, we discuss the performance of classical molecular dynamics in predicting the experimental X-ray diffraction patterns of liquid ethylammonium nitrate (one of the simplest protic room-temperature ionic liquid showing amphiphilic behavior) and of its hydroxy derivative (2-ethanolammonium nitrate, 2-HOEAN). Newly recorded energy-dispersive X-ray diffraction structure factors are compared with the corresponding quantities extracted from molecular dynamics simulations. Other useful theoretical and experimental indicators are used as a probe of the local structure of the title ionic liquids. We shall show that the use of a general purpose, two-body terms only, force field, such as OPLS/AA is able to describe most of the structural experimental data. However, we shall also point out that an improved description of some key structural features observed in the X-ray radial distribution function, can be obtained very easily by adding a general three-body potential energy term instead of changing the two-body potential parameters, in order to optimize the agreement with experimental data. This three-body term turns out to be naturally able to describe the complex polarization effects due to hydrogen bonding without requiring a quanto-mechanical treatment or a polarizable force field. In addition the present model turns out to be able to account for the presence of a low-Q peak in the scattering patterns of EAN, which has been commonly interpreted as a manifestation of the amphiphilic nature of this compound.

The thermal stability of hexylammonium chloride (HeAC) has been investigated in situ real time by high-temperature X-ray powder diffraction. A phase transition from a low-temperature (LT) tetragonal to a high-temperature (HT) cubic polymorph has been detected at 473 K. A first sharp diffraction peak (FSDP) starts to grow at the same temperature and disappears at 493 K, just before melting starts to occur. The dependence of cell parameters from temperature has been quantified for the LT polymorph and shown to be very anisotropic. In particular, the tetragonal a parameter expands, while the c parameter contracts, and as a net result, the volume increases. The HT polymorph shows features reminiscent of that of plastic phases of molecular crystals and is characterized by a less efficient packing as compared to the LT polymorph as indicated by a volume expansion of ca. 11%. Moreover, the structural properties of HeAC/water mixtures, up to very high dilution, have been investigated by combining MD simulations and X-ray diffraction experiments. By using a Cl-water Lennard-Jones parameter previously refined for a similar system, a very good agreement between the theoretical and experimental diffraction patterns was obtained for all the studied systems. The Cl(-) ions in the mixtures were found to form both a first and second shell of water molecules. Moreover, a complex structural behavior has been highlighted, in which a strong interaction between cations and anions survives also in conditions of very high dilution. As a consequence, cations and anions do not always possess a completely closed hydration shell of their own, but rather solvent-shared ion pairs are formed to some extent in all the investigated mixtures., (© 2012 American Chemical Society)

X-ray absorption near-edge structure (XANES) spectroscopy and molecular dynamics (MD) simulations have been jointly applied to the study of the Cu,Zn superoxide dismutase from Haemophilus ducreyi (HdSOD) in interaction with the carbon monoxide molecule. The configurational flexibility of the Fe(II)-heme group, intercalated between the two subunits, has been sampled by MD simulations and included in the XANES data analysis without optimization in the structural parameter space. Our results provide an interpretation of the observed discrepancy in the Fe-heme distances as detected by extended X-ray absorption fine structure (EXAFS) spectroscopy and the classical XANES analysis, in which the structural parameters are optimized in a unique structure. Moreover, binding of the CO molecule to the heme induces a long range effect on the Cu,Zn active site, as evidenced by both MD simulations and in vitro experiments. MD simulation of the CO bound system, in fact, highlighted a structural rearrangement of the protein-protein hydrogen bond network in the region of the Cu,Zn active site, correlated with an increase in water accessibility at short distance from the copper atom. In line, in vitro experiments evidenced an increase of copper accessibility to a chelating agent when the CO molecule binds to the heme group, as compared to a heme deprived HdSOD. Altogether, our results support the hypothesis that the HdSOD is a heme-sensor protein, in which binding to small gaseous molecules modulates the enzyme superoxide activity as an adaptive response to the bacterial environment.

The thermal behavior of propylammonium chloride (PAC) has been investigated by parallel beam X-ray powder diffraction in the 303-463 K thermal range. A polymorphic transition has been observed at 403 K, whereas the melting process starts at 438 K. The low-temperature (LT) polymorph is tetragonal, P4/n or P4/nmm, and a = 6.2429(2) Å, c = 7.3830(3) Å, and Z = 2. Thermal expansion is isotropic as the N···Cl interactions have components along the three crystallographic axes. At the transition temperature, a high-temperature (HT) polymorph was observed, with candidate space groups P23, Pm3, P432, P43m, and Pm3m and cell parameter a = 11.715(3) Å, consistent with Z = 12. This phase has features reminiscent of those of plastic phases of molecular crystals. The structural properties of a PAC/water mixture at ambient conditions were also studied by using an integrated approach, which combines X-ray diffraction measurements and molecular dynamics simulations carried out with the SPC/E and TIP5P water models. By using a Cl-water Lennard-Jones parameter previously refined for a similar system, a very good agreement between the theoretical and experimental diffraction patterns was obtained, especially in the case of the TIP5P simulation. A complex structural behavior has been highlighted, in which cations and anions do not possess a completely closed hydration shell of their own, but rather "solvent-shared ion pairs" are formed, where one or more water molecules act as a bridge between the chloride and propylammonium ions.

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.