The aqueous Ca2+ system, in comparison with Zn2+, Fe3+, and Al3+: an ab initio molecular dynamics study

Hydration Structure of 102No2+: A Density Functional Theory-Molecular Dynamics Study

The hydration structure of No2+, the divalent cation of nobelium in water, was investigated by ab initio molecular dynamics (MD) simulations. First, a series of benchmark calculations were performed to validate the density functional theory (DFT) calculation methods for a molecule containing a No atom. The DFT-MD simulation of the hydration structure of No2+ was conducted after the MD method was validated by simulating the hydration structures of Ca2+ and Sr2+, whose behavior was previously reported to be similar to that of No2+. The model cluster containing M2+ (M = Ca, Sr, or No) and 32 water molecules was used for DFT-MD simulation. The results showed that the hydration distance of No2+ was intermediate between those of Ca2+ and Sr2+. This trend in the hydration distance is in good agreement with the elution position trend obtained in a previous radiochemical experiment. The calculated No-O bond lengths in the optimized structure of [No(H2O)8]2+ was 2.59 Å, while the average No-O bond length of [No(H2O)8]2+ in water by DFT-MD was 2.55 Å. This difference implies the importance of dynamic solvent effects, considering the second (and further) coordination sphere in the theoretical calculation of solution chemistry for superheavy elements.

On Local Structure Equilibration of Ca2+ in Solution by Ab Initio Molecular Dynamics

Analyzing the stable isotopic ratio of Ca offers valuable insights into a wide range of applications from climate reconstruction to bone cancer diagnosis and agricultural nutrient improvement. While the first hydration shell of Ca in solution is expected to play a major role in its fractionation properties, the coordination of Ca in water remains a subject of debate. In this work, Ca2+ in water has been modeled by means of ab initio molecular dynamics simulations using various exchange and correlation functionals and at different temperatures. Results show a significant effect of the functional on the average Ca2+ coordination, depending on its tendency to over- or understructure liquid water. The BLYP functional with Grimme-D2 correction was judged as the most accurate among those tested based on its accuracy to reproduce water structural and diffusion properties. Using this functional, the effect of temperature has been systematically investigated, focusing on means to limit the uncertainty in our assessments of the average coordination of Ca2+ ions by (1) estimating the number of water exchanges in the simulations and (2) implementing a statistical approach based on Markov chains. The findings indicate, especially, that our simulations at 300, 350, and 400 K do not yield converged results due to potential equilibration problems. These observations impose substantial constraints on the trustworthiness of numerous estimates in the existing literature that depend on trajectories with insufficient exchanges. We estimate Ca2+ coordination values of 6.8 ± 0.1, 6.8 ± 0.1, 6.7 ± 0.2, and 6.7 ± 0.2 at 600, 550, 500, and 450 K respectively. At lower temperatures (300, 350, and 400 K), while obtaining definitive values for Ca2+ coordination remains challenging, our research does indicate a potential temperature-related influence on coordination with an average Ca2+ coordination at 300 K as low as 6.2.

Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel

The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are neurotransmitter-activated cation channels ubiquitously expressed in vertebrate brains. The regulation of calcium flux through the channel pore by RNA-editing is linked to synaptic plasticity while excessive calcium influx poses a risk for neurodegeneration. Unfortunately, the molecular mechanisms underlying this key process are mostly unknown. Here, we investigated calcium conduction in calcium-permeable AMPAR using Molecular Dynamics (MD) simulations with recently introduced multisite force-field parameters for Ca²⁺. Our calculations are consistent with experiment and explain the distinct calcium permeability in different RNA-edited forms of GluA2. For one of the identified metal binding sites, multiscale Quantum Mechanics/Molecular Mechanics (QM/MM) simulations further validated the results from MD and revealed small but reproducible charge transfer between the metal ion and its first solvation shell. In addition, the ion occupancy derived from MD simulations independently reproduced the Ca²⁺ binding profile in an X-ray structure of an NaK channel mimicking the AMPAR selectivity filter. This integrated study comprising X-ray crystallography, multisite MD, and multiscale QM/MM simulations provides unprecedented insights into Ca²⁺ permeation mechanisms in AMPARs, and paves the way for studying other biological processes in which Ca²⁺ plays a pivotal role.

Association of Defects and Zinc in Hematite

Zn is an essential micronutrient that is often limited in tropical, lateritic soils in part because it is sequestered in nominally refractory iron oxide phases. Stable phases such as goethite and hematite, however, can undergo reductive recrystallization without a phase change under circumneutral pH conditions and release metal impurities such as Zn into aqueous solutions. Further, the process appears to be driven by Fe vacancies. In this contribution, we used ab initio molecular dynamics informed extended X-ray absorption fine structure spectra to show that Zn incorporated in the structure of hematite is associated with coupled O-Fe and protonated Fe vacancies, providing a potential link between crystal chemistry and the bioavailability of Zn.

Ab initio molecular dynamics studies of hydroxide coordination of alkaline earth metals and uranyl

Ab initio molecular dynamics (AIMD) simulations of the Mg2+, Ca2+, Sr2+ and UO22+ ions in either a pure aqueous environment or an environment containing two hydroxide ions have been carried out at the density functional level of theory, employing the generalised gradient approximation via the PBE exchange-correlation functional. Calculated mean M-O bond lengths in the first solvation shell of the aquo systems compared very well to existing experimental and computational literature, with bond lengths well within values measured previously and coordination numbers in line with previously calculated values. When applied to systems containing additional hydroxide ions, the methodology revealed increased bond lengths in all systems. Proton transfer events (PTEs) were recorded and were found to be most prevalent in the strontium hydroxide systems, likely due to the low charge density of the ion and the consequent lack of hydroxide coordination. For all alkaline earths, intrashell PTEs which occurred outside of the first solvation shell were most prevalent. Only three PTEs were identified in the entire simulation data of the uranium dihydroxide system, indicating the clear impact of the increased charge density of the hexavalent uranium ion on the strength of metal-oxygen bonds in aqueous solution. Broadly, systems containing more charge dense ions were found to exhibit fewer PTEs than those containing ions of lower charge density.

Microscopic insight into precipitation and adsorption of As(V) species by Fe-based materials in aqueous phase

The mechanism of As(V) removal from the drinking water and industrial effluents by iron materials remains unclear at the molecular level. In this work, the association of Fe-based materials with As(V) species was explored using density functional theory and ab initio calculations. Solvent separated ion pair structures of [FeH₂AsO₄]²⁺_aq species may be dominant in an acidic solution of FeAs complex. The association trend of H₂AsO₄^- species by Fe³⁺_aq is found to be quite weak in the aqueous solution, which may be attributed to the strong hydration of Fe³⁺_aq and [FeH₂AsO₄]²⁺ species. However, the association of H₂AsO₄^- species by colloidal clusters is quite strong, due to the weakened hydration of Fe(III) in colloidal structures. The hydrophobicity of Fe-based materials may be one of the key factors for their As(V) removal efficiency in an aqueous phase. When the number of OH^- coordinated with Fe(III) increases, the association trend of As(V) by colloidal ferric hydroxides weakens accordingly. This study provides insights into understanding the coprecipitation and adsorption mechanisms of arsenate removal and revealing the high efficiency of arsenate removal by colloidal ferric hydroxides or iron salts under moderate pH conditions.

Water dynamics in hydrated amorphous materials: a molecular dynamics study of the effects of dehydration in amorphous calcium carbonate

Amorphous calcium carbonate (ACC) is often a critical transient phase in the formation of crystalline phases of CaCO₃via dehydration of hydrated ACC. The behavior of the water molecules plays a pivotal role in this transformation. We report here the dynamics of water molecules in ACC at hydration levels from CaCO₃·1H₂O to CaCO₃·0.25H₂O using molecular dynamics (MD) simulations. Due to the presence of highly hydrophilic Ca²⁺ and the strong H-bond acceptor CO₃^2-, most of the water molecules in our simulations have restricted translational and orientational dynamics. These are referred here as 'slow water'. However, a small fraction of them show high diffusivity at all hydration states and are referred here as 'fast water'. The computed diffusion coefficients of the slow waters, as extrapolated from simulation results, yield diffusion distances of the order of μm on the 1 hour time scale, consistent with rapid dehydration of ACC nano-particles in the laboratory. We correlate our fast waters with the water molecules in the percolating water-rich, Ca²⁺-deficient nano-pores in the structure of Goodwin et al. [Chem. Mater., 2010, 22, 3197], obtained by analysis of X-ray scattering data, and our slow waters with those in the Ca²⁺-rich volumes with less water in their model. The fast waters can be considered to be free rotors on the ns time scale and have orders of magnitude shorter rotational relaxation times than the slow waters.

Insights into water-mediated ion clustering in aqueous CaSO4 solutions: pre-nucleation cluster characteristics studied by ab initio calculations and molecular dynamics simulations

The molecular structure of growth units building crystals is a fundamental issue in the crystallization processes from aqueous solutions. In this work, a systematic investigation of pre-nucleation clusters and their hydration characteristics in aqueous CaSO₄ solutions was performed using ab initio calculations and molecular dynamics (MD) simulations. The results of ab initio calculations and MD simulations indicate that the dominant species in aqueous CaSO₄ solutions are monodentate ion-associated structures. Compared with charged ion clusters, neutral clusters are more likely to be present in an aqueous CaSO₄ solution. Neutral (CaSO₄)_m clusters are probably the growth units involved in the pre-nucleation or crystallization processes. Meanwhile, hydration behavior around ion associated species in aqueous CaSO₄ solutions plays an important role in related phase/polymorphism selections. Upon ion clustering, the residence of some water molecules around Ca²⁺ in ion-associated species is weakened while that of some bridging waters is enhanced due to dual interaction by Ca²⁺ and SO₄^2-. Some phase/polymorphism selections can be achieved in aqueous CaSO₄ solutions by controlling the hydration around pre-nucleation clusters. Moreover, the association trend between calcium and sulfate is found to be relatively strong, which hints at the low solubility of calcium sulfate in water.

Supersaturated calcium carbonate solutions are classical

Mechanisms of CaCO₃ nucleation from solutions that depend on multistage pathways and the existence of species far more complex than simple ions or ion pairs have recently been proposed. Herein, we provide a tightly coupled theoretical and experimental study on the pathways that precede the initial stages of CaCO₃ nucleation. Starting from molecular simulations, we succeed in correctly predicting bulk thermodynamic quantities and experimental data, including equilibrium constants, titration curves, and detailed x-ray absorption spectra taken from the supersaturated CaCO₃ solutions. The picture that emerges is in complete agreement with classical views of cluster populations in which ions and ion pairs dominate, with the concomitant free energy landscapes following classical nucleation theory.

Force Field Parametrization of Metal Ions from Statistical Learning Techniques

A novel statistical procedure has been developed to optimize the parameters of nonbonded force fields of metal ions in soft matter. The criterion for the optimization is the minimization of the deviations from ab initio forces and energies calculated for model systems. The method exploits the combination of the linear ridge regression and the cross-validation techniques with the differential evolution algorithm. Wide freedom in the choice of the functional form of the force fields is allowed since both linear and nonlinear parameters can be optimized. In order to maximize the information content of the data employed in the fitting procedure, the composition of the training set is entrusted to a combinatorial optimization algorithm which maximizes the dissimilarity of the included instances. The methodology has been validated using the force field parametrization of five metal ions (Zn²⁺, Ni²⁺, Mg²⁺, Ca²⁺, and Na⁺) in water as test cases.

Real single ion solvation free energies with quantum mechanical simulation

Single ion solvation free energies are one of the most important properties of electrolyte solutions and yet there is ongoing debate about what these values are. Only the values for neutral ion pairs are known. Here, we use DFT interaction potentials with molecular dynamics simulation (DFT-MD) combined with a modified version of the quasi-chemical theory (QCT) to calculate these energies for the lithium and fluoride ions. A method to correct for the error in the DFT functional is developed and very good agreement with the experimental value for the lithium fluoride pair is obtained. Moreover, this method partitions the energies into physically intuitive terms such as surface potential, cavity and charging energies which are amenable to descriptions with reduced models. Our research suggests that lithium's solvation free energy is dominated by the free energetics of a charged hard sphere, whereas fluoride exhibits significant quantum mechanical behavior that cannot be simply described with a reduced model.

Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations

BACKGROUND

Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite [α-Fe(OOH)]. Ab initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Several exchange correlation functionals were employed (PBE96, PBE96 + Grimme, and PBE0) in the simulations of a (3 × 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a = 30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick).

RESULTS

The lowest energy goethite (100) surface termination model was determined to have an exposed surface Fe³⁺ that was loosely capped by a water molecule and a shared hydroxide with a neighboring surface Fe³⁺. The water molecules capping surface Fe³⁺ ions were found to be loosely bound at all DFT levels with and without Grimme corrections, indicative that each surface Fe³⁺ was coordinated with only five neighbors. These long bonds were supported by bond valence theory calculations, which showed that the bond valence of the surface Fe³⁺ was saturated and surface has a neutral charge. The polarization of the water layer adjacent to the surface was found to be small and affected only the nearest water. Analysis by density difference plots and localized Boys orbitals identified three types of water molecules: those loosely bound to the surface Fe³⁺, those hydrogen bonded to the surface hydroxyl, and bulk water with tetrahedral coordination. Boys orbital analysis showed that the spin down lone pair orbital of the weakly absorbed water interact more strongly with the spin up Fe³⁺ ion. These weakly bound surface water molecules were found to rapidly exchange with the second water layer (~0.025 exchanges/ps) using a dissociative mechanism.

CONCLUSIONS

Water molecules adjacent to the surface were found to only weakly interact with the surface and as a result were readily able to exchange with the bulk water. To account for the large surface Fe-OH₂ distances in the DFT calculations it was proposed that the surface Fe³⁺ atoms, which already have their bond valence fully satisfied with only five neighbors, are under-coordinated with respect to the bulk coordination. Graphical abstract All first principle calculations, at all practically achievable levels, for the goethite 100 aqueous interface support a long bond and weak interaction between the exposed surface Fe³⁺ and water molecules capping the surface. This result is supported by bond valence theory calculations and is indicative that each surface Fe³⁺ is coordinated with only 5 neighbors.

Asymmetric hydration structure around calcium ion restricted in micropores fabricated in activated carbons

The adsorbed phase and hydration structure of an aqueous solution of Ca(NO3)2 restricted in micropores fabricated in activated carbons (ACs) having different average pore widths (0.63 and 1.1 nm) were investigated with the analysis of adsorption isotherms and x-ray absorption fine structure (XAFS) spectra on Ca K-edge. The adsorbed density of Ca(2+) per unit micropore volume in the narrower pore was higher than in the wider pore, while the adsorbed amount per unit mass of carbon with the narrower pore was half of the amount of ACs with the larger pore. On the other hand, variations in the bands assigned to double-electron (KM I) and 1s  →  3d excitations in XAFS spectra demonstrate the formation of a distorted hydration cluster around Ca(2+) in the micropore, although the structural parameters of hydrated Ca(2+) in the micropores were almost consistent with the bulk aqueous solution, as revealed by the analysis of extended XAFS (EXAFS) spectra. In contrast to the hydration structure of monovalent ions such as Rb(+), which generally presents a dehydrated structure in smaller than 1 nm micropores in ACs, the present study clearly explains that the non-spherically-symmetric structure of hydrated Ca(2+) restricted in carbon micropores whose sizes are around 1 nm is experimentally revealed where any dehydration phenomena from the first hydration shell around Ca(2+) could not be observed.

Ab Initio Studies of Calcium Carbonate Hydration

Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance.

A metal-enhanced fluorescence sensing platform based on new mercapto rhodamine derivatives for reversible Hg(2+) detection

A new metal-enhanced fluorescence (MEF) chemosensor HMS-Ag-R-2SH for Hg(2+) has been prepared via a simple and effective method. The fluorescent chemosensor was based on a mercapto rhodamine derivatives linked with Ag nanoparticles, and the Ag nanoparticles were supported on hexagonal mesoporous silica material (HMS). Transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), absorption spectroscopy and fluorescence spectroscopy techniques were employed to characterize morphology, mesostructure and spectral features of the chemosensor. This chemosensor works in a nearly pure aqueous solution with a broad pH range. The output signals include color change and fluorescence. Moreover, HMS-Ag-R-2SH presents excellent anti-disturbance ability when exposed to a series of competitive cations such as Ag(+), K(+), Li(+), Na(+), Ba(2+), Ca(2+), Cd(2+), Co(2+), Cu(2+), Mg(2+), Mn(2+), Ni(2+), Pb(2+), Zn(2+), Al(3+), Cr(3+) and Fe(3+). The selectivity of this chemosensor was significantly improved due to the introduction of the sulphydryl. The chemosensor showed a lower detection limit of 2.1ppb for Hg(2+). Importantly, HMS-Ag-R-2SH could be regenerated with sodium sulfide solution for several cycles and maintain a high sensitivity.

Prediction of the pKa's of aqueous metal ion +2 complexes

Aqueous metal ions play an important role in many areas of chemistry. The acidities of [Be(H2O)4](2+), [M(H2O)6](2+), M = Mg(2+), Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), and Hg(2+), and [M(H2O)n](2+), M = Ca(2+) and Sr(2+), n = 7 and 8, complexes have been predicted using density functional theory, second-order Møller-Plesset perturbation theory (MP2), and coupled cluster CCSD(T) theory in the gas phase. pKa's in aqueous solution were predicted by using self-consistent reaction field (SCRF) calculations with different solvation models. The most common binding motif of the majority of the metal +2 complexes is coordination number (CN) 6, with each hexaaquo cluster having reasonably high symmetry for the best arrangement of the water molecules in the first solvation shell. Be(2+) is tetracoordinated, but a second solvation shell of 8 waters is needed to predict the pKa. The Ca(2+) and Sr(2+) aquo clusters have a coordination number of 7 or 8 as found in terms of the energy of the reaction M(H2O)7(2+) + H2O → M(H2O)8(2+) and the pKa values. The calculated geometries are in reasonable agreement with experiment. The SCRF calculations with the conductor-like screening model (COSMO), and the conductor polarized continuum model (CPCM) using COSMO-RS radii, consistently agree best with experiment at the MP2/aug-cc-pVDZ and CCSD(T)/aug-cc-pVDZ levels of theory. The CCSD(T) level provides the most accurate pKa's, and the MP2 level also provides reliable predictions. Our predictions were used to elucidate the properties of metal +2 ion complexes. The pKa predictions provide confirmation of the size of the first solvation shell sizes. The calculations show that it is still difficult to predict pKa's using this cluster/implicit solvent approach to better than 1 pKa unit.

Vibrational models for a crystal with 36 water molecules in the unit cell: IR spectra from experiment and calculation

One dimensional uncoupled anharmonic approach for modeling water OH stretchings in crystalline hydrates.

Large polarization but small electron transfer for water around Al(3+) in a highly hydrated crystal

Precise molecular-level information on the water molecule is precious, since it affects our interpretation of the role of water in a range of important applications of aqueous media. Here we propose that electronic structure calculations for highly hydrated crystals yield such information. Properties of nine structurally different water molecules (19 independent OO hydrogen bonds) in the Al(NO3)3·9H2O crystal have been calculated from DFT calculations. We combine the advantage of studying different water environments using one and the same compound and method (instead of comparing a set of independent experiments, each with its own set of errors) with the advantage of knowing the exact atomic positions, and the advantage of calculating properties that are difficult to extract from experiment. We find very large Wannier dipole moments for H2O molecules surrounding the cations: 4.0-4.3 D (compared to our calculated value of 1.83 D in the gas phase). These are induced by the ions and the H-bonds, while other water interactions and the relaxation of the internal water geometry in fact decrease the dipole moments. We find a good correlation between the water dipole moment and the OO distances, and an even better (non-linear) correlation with the average electric field over the molecule. Literature simulation data for ionic aqueous solutions fit quite well with our crystalline 'dipole moment vs. OO distance' curve. The progression of the water and cation charges from 'small clusters ⇒ large clusters ⇒ the crystal' helps explain why the net charges on all the water molecules are so small in the crystal.

On the coupling of solvent characteristics to the electronic structure of solute molecules

We present the results of a theoretical investigation focusing on the solvent structure surrounding the -1, 0 and +1 charged species of F, Cl, Br and I halogen atoms and F2, Cl2, Br2 and I2 di-halogen molecules in a methanol solvent and its influence on the electronic structure of the solute molecules. Our results show a large stabilizing effect arising from the solute-solvent interactions. Well-formed first solvation shells are observed for all species, the structure of which is strongly influenced by the charge of the solute species. Detailed analysis reveals that coordination number, CN, solvent orientation, θ, and solute-solvent distance, d, are important structural characteristics which are coupled to changes in the electronic structure of the solute. We propose that the fundamental chemistry of any solute species is generally regulated by these solvent degrees of freedom.

Coordination and hydrolysis of plutonium ions in aqueous solution using Car-Parrinello molecular dynamics free energy simulations

Car-Parrinello molecular dynamics (CPMD) simulations have been used to examine the hydration structures, coordination energetics, and the first hydrolysis constants of Pu(3+), Pu(4+), PuO2(+), and PuO2(2+) ions in aqueous solution at 300 K. The coordination numbers and structural properties of the first shell of these ions are in good agreement with available experimental estimates. The hexavalent PuO2(2+) species is coordinated to five aquo ligands while the pentavalent PuO2(+) complex is coordinated to four aquo ligands. The Pu(3+) and Pu(4+) ions are both coordinated to eight water molecules. The first hydrolysis constants obtained for Pu(3+) and PuO2(2+) are 6.65 and 5.70, respectively, all within 0.3 pH unit of the experimental values (6.90 and 5.50, respectively). The hydrolysis constant of Pu(4+), 0.17, disagrees with the value of -0.60 in the most recent update of the Nuclear Energy Agency Thermochemical Database (NEA-TDB) but supports recent experimental findings. The hydrolysis constant of PuO2(+), 9.51, supports the experimental results of Bennett et al. [Radiochim. Acta 1992, 56, 15]. A correlation between the pKa of the first hydrolysis reaction and the effective charge of the plutonium center was found.