The feasibility of a novel approach for the hybrid quantum mechanical/molecular mechanical (QM/MM) treatment of solid-state surfaces without the requirement of artificially keeping atoms at fixed positions is explored. In order to avoid potential artifacts of the QM/MM transition near the surface, a 2d-periodic QM treatment of the system is employed. Thus, the only QM/MM interface between atoms of the solid is along the non-periodic z-dimension. It is shown for the metal oxide and metal systems MgO(100) and Be(0001) that a properly adjusted embedding potential supplemented by adequate non-Coulombic potentials (if required) enables the application of the QM/MM framework in all-atom structure optimization and molecular dynamics (MD) simulation. The commonly employed constraint to keep at least some of the embedding atoms at fixed position is not required. Two exemplary applications of H2O on MgO(100) and H2 on Be(0001) demonstrate the applicability of the framework in exemplary MD simulation studies.
A theoretical study of the structure and dynamics of the uranyl mono- and dicarbonate species in aqueous solution employing the quantum mechanical charge field-molecular dynamics (QMCF-MD) method is presented. The obtained structural and dynamical data were found to be in good agreement with several experimental data and theoretical investigations available in the literature. The five-fold coordination pattern observed for the equatorially bounded ligands of the uranyl ion was found to deviate from the results of a number of previous studies based on quantum chemical cluster calculations and classical molecular dynamics studies, however. The reason for the different description of the system can be seen on the one hand in the capability of QM/MM-type simulations to take charge transfer, polarization, and many-body effects into account, while the presence of a large number of MM solvent molecules ensures that the simulation system mimics the environment in the bulk of a liquid. In addition to pair, three-body and angular distributions, the use of spatial density data enabled a detailed characterization of the three-dimensional arrangement of ligands in the vicinity of the complex. Further analysis of dynamical data such as hydrogen-bond correlation functions and mean lifetime analysis enabled a detailed characterization of the properties of the complexes in aqueous solution. It could be shown that the bulk-oriented oxygen atoms of the carbonate ions form strong hydrogen bonds with bulk molecules, while the tendency of the oxygen atoms of the uranyl(VI) show decreasing tendency to form hydrogen bonds upon complexation.
This investigation presents the characterization of structural and dynamical properties of uranyl tricarbonate in aqueous solution employing an extended hybrid quantum mechanical/molecular mechanical (QM/MM) approach. It is shown that the inclusion of explicit solvent molecules in the quantum chemical treatment is essential to mimic the complex interaction occurring in an aqueous environment. Thus, in contrast to gas phase cluster calculations on a quantum chemical level proposing a 6-fold coordination of the three carbonates, the QMCF MD simulation proposes a 5-fold coordination. An extensive comparison of the simulation results to structural and dynamical data available in the literature was found to be in excellent agreement. Furthermore, this work is the first theoretical study on a quantum chemical level of theory able to observe the conversion of carbonate (CO₃²⁻) to bicarbonate (HCO₃⁻) in the equatorial coordination sphere of the uranyl ion. From a comparison of the free energy ΔG values for the unprotonated educt [UO₂(CO₃)₃]⁴⁻ and the protonated [UO₂(CO₃)₂(HCO₃)]³⁻, it could be concluded that the reaction equilibrium is strongly shifted toward the product state confirming the benignity for the observed protonation reaction. Structural properties and the three-dimensional arrangement of carbonate ligands were analyzed via pair-, three-body, and angular distributions, the dynamical properties were evaluated by hydrogen-bond correlation functions and vibrational power spectra.
A combined theoretical and experimental study has been performed to elucidate the structural and dynamical properties of aqueous hexacyanoferrate(II) isolated and in presence of potassium ions. It is shown that in absence of counter ions, the highly negatively charged hexacyanoferrate(II) complex is not stable in aqueous solution.However, if the high negative charge is compensated by potassium counter ions, a stable complex is observed, which is proven by theoretical simulations as well as by EXAFS experiments. From the simulation it is found that potassium ions surrounding the complex are highly mobile and thus, cannot be observed in the experiment. The structure of aqueous hexacyanoferrate(II) in presence of potassium ions is identical to that of the solid state structure, but the mobility of potassium ions is significantly increased in the liquid. These highly mobile potassium ions circulating the complex should be the reason for the very short hydrogen bond lifetimes in the femtosecond range of the cyanide ligands.
, x=3-8, and radial distribution functions from simulation of the thiosulfate ion, and from experimental LAXS data on the hydrated peroxodisulfate ion in water. Graphical Abstract SynopsisExperimental and simulation data of the thiosulfate ion show large similarities in hydration structure and mechanism with the sulfate ion but with weaker hydration of the terminal sulfur atom in thiosulfate. AbstractTheoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) to study the structure and dynamics of the hydrated thiosulfate ion, S 2 O 3 2-, in aqueous solution. The S-O and S C -S T bond distances have been determined to 1.479(5) and 2.020(6) Å by LAXS and to 1.478 and 2.017 Å by QMCF MD simulations, which are slightly longer than the mean values found in the solid state, 1.467 and 2.002 Å, respectively. This is due to the hydrogen bonds formed at hydration.The water dynamics show that water molecules are exchanged at the hydrated oxygen and sulfur atoms, and that the water exchange is ca. 50% faster at the sulfur atom than at the oxygens atoms with mean residence times, 0.5 , of 2.4 and 3.6 ps, respectively. From this point of view the water exchange dynamics mechanism resembles the sulfate ion, while it is significantly different from the sulfite ion. This shows that the lone electron-pair in the sulfite ion has a much larger impact on the water exchange dynamics than a substitution of an oxygen atom for a sulfur one. The LAXS data did give mean S C ⋅⋅⋅O aq1 and S C ⋅⋅⋅O aq2 distances of 3.66(2) and 4.36(10) Å, respectively, and S C -O thio and O thio ⋅⋅⋅O aq1 , S C -S T and S T ⋅⋅⋅O aq2 distances of 1.479(5), 2.845(10), 2.020(6) and 3.24(5) Å, respectively, giving S C -O thio ⋅⋅⋅O aq1 and S C -S T ⋅⋅⋅O aq2 angles close 110 o , strongly indicating a tetrahedral geometry around the terminal thiosulfate sulfur and the oxygens, and thereby, three water molecules are hydrogen bound to each of them. The hydrogen bonds between thiosulfate oxygens and the hydrating water molecules are stronger and with longer mean residence times than between water molecules in the aqueous bulk, while the opposite is true for the hydrogen bonds between the terminal thiosulfate sulfur and the hydrating water molecules. The hydration of all oxo sulfur ions are discussed using the detailed observations for the sulfate, thiosulfate and sulfite ions, and the structure of the hydrated peroxodisulfate ion, S 2 O 8 2-, in aqueous solution has been determined by means of LAXS to support the general observations. The mean S-O bond distances are 1.448(2) and 1.675(5) Å to the oxo and peroxo oxygens, respectively.
The presented study elucidates the influence of calcium(II) counter-ions on the structure of the environmentally relevant uranyl tricarbonates using hybrid quantum mechanical/molecular mechanical (QM/MM) MD simulations. Since experimental investigations may be subject to limitations in detecting the presence of counter-ions in solution, the present study is of importance to obtain a profound understanding of the effects counter-ions may have on coordination complexes. It can be concluded from the obtained simulation data that two calcium(II) ions are essential for stabilizing the experimentally observed uranyl tricarbonate complex in aqueous solution. Including only one calcium(II) ion in the coordination sphere was found to be insufficient to form a six-fold equatorial coordination of carbonates, but a five-fold coordination is adopted similar to the counter-ion free case in aqueous solution reported in a previous study.
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