Structural convergence properties of amorphous InGaZnO4 from simulated liquid-quench methods.

The study of structural properties of amorphous structures is complicated by the lack of long-range order and necessitates the use of both cutting-edge computer modeling and experimental techniques. With regards to the computer modeling, many questions on convergence arise when trying to assess the accuracy of a simulated system. What cell size maximizes the accuracy while remaining computationally efficient? More importantly, does averaging multiple smaller cells adequately describe features found in bulk amorphous materials? How small is too small? The aims of this work are: (1) to report a newly developed set of pair potentials for InGaZnO4 and (2) to explore the effects of structural parameters such as simulation cell size and numbers on the structural convergence of amorphous InGaZnO4. The total number of formula units considered over all runs is found to be the critical factor in convergence as long as the cell considered contains a minimum of circa fifteen formula units. There is qualitative agreement between these simulations and X-ray total scattering data - peak trends and locations are consistently reproduced while intensities are weaker. These new IGZO pair potentials are a valuable starting point for future structural refinement efforts.

The energetics of isomerisation in Keggin-series aluminate cations.

Electronic-structure calculations show that the ε-isomer of the polyoxoaluminate ion in the Keggin structure [AlO4-(Al(OH)2(H2O))12](7+) is the thermodynamically favoured one. Direct interconversion between the ε- and δ-isomers via cap rotation has a prohibitively high energy barrier in vacuo, suggesting that isomerisation in solution either proceeds via a dissolution-precipitation pathway, or that solvation and/or coordination to counterions reduces the barrier significantly. The implications for the formation of the [Al2O8Al28(OH)56(H2O)26](18+) ion are discussed.

Metastable structures and isotope exchange reactions in polyoxometalate ions provide a molecular view of oxide dissolution.

Reactions involving minerals and glasses in water are slow and difficult to probe spectroscopically but are fundamental to the performance of oxide materials in green technologies such as automotive thermoelectric power generation, CO2 capture and storage and water-oxidation catalysis; these must be made from geochemically common elements and operate in hydrous environments. Polyoxometalate ions (POMs) have structures similar to condensed oxide phases and can be used as molecular models of the oxide/water interface. Oxygen atoms in POM exchange isotopes at different rates, but, at present, there is no basis for predicting how the coordination environment and metal substitution influences rates and mechanisms. Here we identify low-energy metastable configurations that form from the breaking of weak bonds between metals and underlying highly coordinated oxygen atoms, followed by facile hydroxide, hydronium or water addition. The mediation of oxygen exchange by these stuffed structures suggests a new view of the relationship between structure and reactivity at the oxide/solution interface.

Peak nothing: recent trends in mineral resource production.

The Hubbert-type analysis used to analyze the production history of oil is applied here to other raw materials. Many resources commonly thought of as being close to "peaking" such as lithium, helium, copper, and the rare earth elements, show no evidence of logistic behavior at any point in their production histories. Although many resources have exhibited logistic behavior in the past, many now show exponential or superexponential growth. In most cases, the transition has occurred in the last ten to twenty years.

17O NMR and computational study of a tetrasiliconiobate ion, [H(2+x)Si4Nb16O56](14-x)-.

Rates of oxygen-isotope exchange were measured in the tetrasiliconiobate ion [H(2+x)Si(4)Nb(16)O(56)]((14-x)-) to better understand how large oxide ions interact with water. The molecule has 19 nonequivalent oxygen sites and is sufficiently complex to evaluate hypotheses derived from our previous work on smaller clusters. We want to examine the extent to which individual oxygen atoms react independently with particular attention given to the order of protonation of the various oxygen sites as the pH decreases from 13 to 6. As in our previous work, we find that the set of oxygen sites reacts at rates that vary over approximately 10(4) across the molecule at 6

Influence of explicit hydration waters in calculating the hydrolysis constants for geochemically relevant metals.

The effect of including a second, explicit solvation shell of water molecules is examined on the DFT calculation of a selection of aquo-metal ions' pK(a) values (deprotonation constants). Our goal is to gauge the accuracy of how certain cluster approximations and implicit solvation models (PCM or COSMO) affect the results. The ions in this study include: Al(3+)((aq)); Fe(3+)((aq)); Cr(3+)((aq)); Mn(3+)((aq)); Co(3+)((aq)); Ga(3+)((aq)); Fe(2+)((aq)); Mg(2+)((aq)); and Be(2+)((aq)). Overall, we find that experimental pK(a) constants can be calculated successfully to within 1-2 pH units, provided a consistent hydration structure is maintained for products and reactants.

Dissolution of insulating oxide materials at the molecular scale.

Our understanding of mineral and glass dissolution has advanced from simple thermodynamic treatments to models that emphasize adsorbate structures. This evolution was driven by the idea that the best understanding is built at the molecular level. Now, it is clear that the molecular questions cannot be answered uniquely with dissolution experiments. At the surface it is unclear which functional groups are present, how they are arranged, and how they interact with each other and with solutes as the key bonds are activated. An alternative approach has developed whereby reactions are studied with nanometre-sized aqueous oxide ions that serve as models for the more complicated oxide interface. For these ions, establishing the structure is not a research problem in itself, and bond ruptures and dissociations can be followed with much confidence. We review the field from bulk-dissolution kinetics to the new isotope-exchange experiments in large oxide ions.

Prediction of iron-isotope fractionation between hematite (alpha-Fe2O3) and ferric and ferrous iron in aqueous solution from density functional theory.

Density functional theory electronic structure calculations are used to compute equilibrium constants for iron-isotope exchange among Fe2+(aq), Fe3+(aq), and hematite (alpha-Fe2O3). The hematite is represented in both bulk and surface environments. The iron-isotope fractionation between Fe2+(aq) and Fe3+(aq), determined using a range of exchange-correlation functionals and basis sets, is in good agreement with experimental measurements. The calculated reduced partition function ratio for bulk hematite is very close to previous estimates based on Mossbauer and inelastic nuclear resonance X-ray spectroscopy. However, the calculated fractionation between hematite bulk and the aqueous species Fe3+(aq) and Fe2+(aq) differs from experimental measurements carried out at the aqueous-hematite interface. We find a heavy iron enrichment trend in the order Fe2+(aq) < hematite bulk approximately hematite surface < Fe3+(aq). In contrast to experimental studies, we find a significant positive fractionation (heavy enrichment) for Fe(3+)(aq) relative to hematite, regardless of whether the hematite is represented by a bulk or a surface model. Our calculations indicate that it is unlikely that the aqueous interfacial structure of hematite is a simple termination of the bulk structure.

Isotope-exchange dynamics in isostructural decametalates with profound differences in reactivity.

Rates of oxygen-isotope exchange at all structural sites in two isostructural polyoxometalates, [H(x)Nb(10)O(28)]((6-x)-) and [H(x)Ti(2)Nb(8)O(28)]((8-x)-), show that small changes in structure have surprising and profound effects: a single-site substitution of Ti(IV) for Nb(V) inverts the pH dependencies for rates throughout the structures. Within a given structure, all oxygens exhibit similar pH dependencies although they react over a range greater than approximately 10(4), indicating that pathways involve concerted motions of the entire lattices. Profound sensitivity to changes in structure and composition suggests reaction pathways in polyoxometalate ions will be highly variable even within structural classes. The results also require new thinking about how ab initio simulations are used to understand reaction pathways involving extended structures, like the mineral-water interface. Our data indicate that reactions proceed via metastable intermediates and that the simulations must be structurally faithful or will miss the essential chemistry.

Minerals as molecules--use of aqueous oxide and hydroxide clusters to understand geochemical reactions.

Large aqueous oxide ions as minerals! Minerals dissolve by repeated ligand exchange reactions and geochemists use polyoxometalate ions to establish structure-reactivity relations for environmentally important functional groups. Here, for example, are plotted the dissolution rates of two classes of minerals against rates of solvent exchanges around the corresponding aquo ions.Geochemists and environmental chemists make predictions about the fate of chemicals in the shallow earth over enormously long times. Key to these predictions is an understanding of the hydrolytic and complexation reactions at oxide mineral surfaces that are difficult to probe spectroscopically. These minerals are usually oxides with repeated structural motifs, like silicate or aluminosilicate polymers, and they expose a relatively simple set of functional groups to solution. The geochemical community is at the forefront of efforts to describe the surface reactivities of these interfacial functional groups and some insights are being acquired by using small oligomeric oxide molecules as experimental models. These small nanometer-size clusters are not minerals, but their solution structures and properties are better resolved than for minerals and calculations are relatively well constrained. The primary experimental data are simple rates of steady oxygen-isotope exchanges into the structures as a function of solution composition that can be related to theoretical results. There are only a few classes of large oxide ions for which data have been acquired and here we review examples and illustrate the general approach, which also derives directly from the use of model clusters to understand for the active core of metalloenzymes in biochemistry.

Theoretical determination of the NMR spectrum of liquid ethanol.

Gauge-invariant NMR chemical shifts of the C and H sites in ethanol is calculated over a variety of conformational and solvation environments using density functional methods. The effects of different exchange and correlation functionals and different basis sets are systematically explored. While there is often a good correlation between atomic charges, as calculated using population analysis techniques, and calculated chemical shifts, we show that calculated populations can only be used as a rough guide to estimating the magnitude of the chemical shift. To incorporate solvent, we use configurations sampled from a classical molecular dynamics simulation of solvated ethanol. We show that the calculated NMR chemical shift at the alcohol proton converges to the experimental result provided that a sufficient number of solvent molecules are included in the GIAO calculation. The predicted shift is in much better agreement with experiment than the shift predicted from clusters with fully optimized solvation shells because of the tendency of solvents to overbond to the alcohol proton in fully optimized configurations.

Mechanism of the hydration of carbon dioxide: direct participation of H2O versus microsolvation.

Thermochemical parameters of carbonic acid and the stationary points on the neutral hydration pathways of carbon dioxide, CO 2 + nH 2O --> H 2CO 3 + ( n - 1)H 2O, with n = 1, 2, 3, and 4, were calculated using geometries optimized at the MP2/aug-cc-pVTZ level. Coupled-cluster theory (CCSD(T)) energies were extrapolated to the complete basis set limit in most cases and then used to evaluate heats of formation. A high energy barrier of approximately 50 kcal/mol was predicted for the addition of one water molecule to CO 2 ( n = 1). This barrier is lowered in cyclic H-bonded systems of CO 2 with water dimer and water trimer in which preassociation complexes are formed with binding energies of approximately 7 and 15 kcal/mol, respectively. For n = 2, a trimeric six-member cyclic transition state has an energy barrier of approximately 33 (gas phase) and a free energy barrier of approximately 31 (in a continuum solvent model of water at 298 K) kcal/mol, relative to the precomplex. For n = 3, two reactive pathways are possible with the first having all three water molecules involved in hydrogen transfer via an eight-member cycle, and in the second, the third water molecule is not directly involved in the hydrogen transfer but solvates the n = 2 transition state. In the gas phase, the two transition states have comparable energies of approximately 15 kcal/mol relative to separated reactants. The first path is favored over in aqueous solution by approximately 5 kcal/mol in free energy due to the formation of a structure resembling a (HCO 3 (-)/H 3OH 2O (+)) ion pair. Bulk solvation reduces the free energy barrier of the first path by approximately 10 kcal/mol for a free energy barrier of approximately 22 kcal/mol for the (CO 2 + 3H 2O) aq reaction. For n = 4, the transition state, in which a three-water chain takes part in the hydrogen transfer while the fourth water microsolvates the cluster, is energetically more favored than transition states incorporating two or four active water molecules. An energy barrier of approximately 20 (gas phase) and a free energy barrier of approximately 19 (in water) kcal/mol were derived for the CO 2 + 4H 2O reaction, and again formation of an ion pair is important. The calculated results confirm the crucial role of direct participation of three water molecules ( n = 3) in the eight-member cyclic TS for the CO 2 hydration reaction. Carbonic acid and its water complexes are consistently higher in energy (by approximately 6-7 kcal/mol) than the corresponding CO 2 complexes and can undergo more facile water-assisted dehydration processes.

Calculation of site-specific carbon-isotope fractionation in pedogenic oxide minerals.

Ab initio molecular dynamics and quantum chemistry techniques are used to calculate the structure, vibrational frequencies, and carbon-isotope fractionation factors of the carbon dioxide component [CO(2)(m)] of soil (oxy)hydroxide minerals goethite, diaspore, and gibbsite. We have identified two possible pathways of incorporation of CO(2)(m) into (oxy)hydroxide crystal structures: one in which the C(4+) substitutes for four H(+) [CO(2)(m)(A)] and another in which C(4+) substitutes for (Al(3+),Fe(3+)) + H(+) [CO(2)(m)(B)]. Calculations of isotope fractionation factors give large differences between the two structures, with the CO(2)(m)(A) being isotopically lighter than CO(2)(m)(B) by approximately 10 per mil in the case of gibbsite and nearly 20 per mil in the case of goethite. The reduced partition function ratio of CO(2)(m)(B) structure in goethite differs from CO(2)(g) by <1 per mil. The predicted fractionation for gibbsite is >10 per mil higher, close to those measured for calcite and aragonite. The surprisingly large difference in the carbon-isotope fractionation factor between the CO(2)(m)(A) and CO(2)(m)(B) structures within a given mineral suggests that the isotopic signatures of soil (oxy)hydroxide could be heterogeneous.

Calculating geochemical reaction pathways--exploration of the inner-sphere water exchange mechanism in Al(H2O)6(3+)(aq) + nH2O with ab Initio calculations and molecular dynamics.

We have simulated exchange of inner-sphere and bulk water molecules for different sizes of Al3+(aq) clusters, Al(H2O)63+ + nH2O for n = 0, 1, 6, or 12, with ab initio and molecular dynamics simulations, in order to understand how robust the ab initio method is for identifying hydrolytic reaction pathways of particular importance to geochemistry. In contrast to many interfacial reactions, this particular elementary reaction is particularly simple and well-constrained by experiment. Nevertheless, we find that a rich array of parallel reaction pathways depend sensitively on the details of the solvation sphere and structure and that larger clusters are not necessarily better. Inner-sphere water exchange in Al3+(aq) may occur through two Langford-Gray dissociative pathways, one in which the incoming and outgoing waters are cis, the other in which they are trans to one another. A large majority of exchanges in the molecular dynamics simulations occurred via the trans mechanism, in contrast to the predictions of the ab initio method. In Al(H2O)63+ + H2O, the cis mechanism has a transition state of 84.3 kJ/mol, which is in good agreement with previous experimental and ab initio results, while the trans mechanism has only a saddle point with two negative frequencies, not a transition state, at 89.7 kJ/mol. In addition to the exchange mechanisms, dissociation pathways could be identified that were considerably lower in energy than experiment and varied considerably between 60 and 100 kJ/mol, depending on the particular geometry and cluster size, with no clear relation between the two. Ab initio calculations using large clusters with full second coordination spheres (n = 12) were unable to find dissociation or exchange transition states because the network of hydrogen bonds in the second coordination sphere was too rigid to accommodate the outgoing inner-sphere water. Our results indicate that caution should surround ab initio simulation of complicated dynamic processes such as hydrolysis, ion exchange, and interfacial reactions that involve several steps. Dynamic methods of simulation need to accompany static methods such as ab initio calculation, and it is best to consider simulated pathways as hypotheses to be tested experimentally rather than definitive properties of the reaction.

Quantum-chemical calculations of carbon-isotope fractionation in CO2(g), aqueous carbonate species, and carbonate minerals.

Quantum chemical calculations on large supermolecular carbonate-water and carbonate mineral clusters are used to predict equilibrium constants for 13,12C-isotope-exchange reactions between CO2(g), aqueous carbonate species, and the common carbonate minerals. For the aqueous species, we evaluate the influence of the size and conformational variability of the solvation shell, the exchange-correlation functional, and the basis set. The choice of exchange-correlation functional (PBE vs B3LYP), the basis set (6-31G* vs aug-cc-pVDZ), and solvation shell size (first shell only vs first shell and a partial second shell) each produce changes of approximately 5-10 per mil in the reduced partition function ratio. Conformational variability gives rise to a standard error of approximately 0.5 per mil using approximately 10 solute-solvent conformations. The best results are obtained with the B3LYP/aug-cc-pVDZ combination, but because the improvements in the basis set and exchange correlation functional drive the reduced partition function ratios in opposite directions, reasonably good results are also obtained with the PBE/6-31G* combination. To construct molecular clusters representative of mineral environments, a new method is introduced on the basis of conservation of Pauling bond strength. Using these clusters as models for minerals, calculations of mineral-gas and mineral-aqueous carbon-isotope fractionation factors, are in good agreement with experimental measurements. Carbon-isotope fractionation factors for gas, aqueous, and mineral phases are thus integrated into a single theoretical/computational framework.

Rates of oxygen-isotope exchange between sites in the [HxTa6O19](8-x)-(aq) Lindqvist ion and aqueous solutions: comparisons to [HxNb6O19](8-x)-(aq).

Rates of steady oxygen-isotope exchange differ in interesting ways for two sets of structural oxygens in the [HxTa6O19](8-x)-(aq) Lindqvist ion when compared to published data on the [HxNb6O19]8-x(aq) version. Because of the lanthanide contraction, the [HxTa6O19](8-x)-(aq) and [HxNb6O19](8-x)-(aq) ions are virtually isostructural and differ primarily in a full core (Kr vs Xe) and the 4f14 electrons in the [HxTa6O19](8-x)-(aq) ion. For both molecules, both pH-dependent and -independent pathways are evident in isotopic exchange of the 12 mu2-O(H) and 6 eta=O sites. Rate parameters for eta=O exchange at conditions where there is no pH dependence are, for the Ta(V) and Nb(V) versions respectively, K(298)(0) = 2.72 x 10(-5) s(-1) and 9.7 x 10(-6) s(-1), DeltaH = 83.6 +/- 3.2 and 89.4 kJ.mol(-1), and DeltaS = -51.0 +/- 10.6 and -42.9 J.mol(-1).K-1. For the mu2-O sites, K(298)(0) = 1.23 x 10(-6) s(-1), DeltaH = 70.3 +/- 9.7 and 88.0 kJ.mol(-1), and DeltaS = -116.1 +/- 32.7 and -29.4 J.mol(-1).K-1. Protonation of the 6 eta=O sites is energetically unfavored relative to the 12 mu2-O bridges in both molecules, although not equally so. Experimentally, protonation labilizes both the mu2-O(H) and eta=O sites to isotopic exchange in both molecules. Density-functional electronic-structure calculations indicate that proton affinities of structural oxygens in the two molecules differ with the [HxTa6O19](8-x)-(aq) anion having a smaller affinity to protonate than the [HxNb6O19]8-x(aq) ion. This difference in proton affinities is evident in the solution chemistry as pKa = 11.5 for the [HTa6O19]7-(aq) ion and pKa = 13.6 for the [HNb6O19]7-(aq) ion. Most striking is the observation that eta=O sites isotopically equilibrate faster than the mu2-O sites for the [HxTa6O19](8-x)-(aq) Lindqvist ion but slower for the [HxNb6O19](8-x)-(aq) ion, indicating that predictions about site reactivities in complicated structures, such as the interface of aqueous solutions and oxide solids, should be approached with great caution.

Interaction between water molecules and zinc sulfide nanoparticles studied by temperature-programmed desorption and molecular dynamics simulations.

We have investigated the bonding of water molecules to the surfaces of ZnS nanoparticles (approximately 2-3 nm sphalerite) using temperature-programmed desorption (TPD). The activation energy for water desorption was derived as a function of the surface coverage through kinetic modeling of the experimental TPD curves. The binding energy of water equals the activation energy of desorption if it is assumed that the activation energy for adsorption is nearly zero. Molecular dynamics (MD) simulations of water adsorption on 3 and 5 nm sphalerite nanoparticles provided insights into the adsorption process and water binding at the atomic level. Water binds with the ZnS nanoparticle surface mainly via formation of Zn-O bonds. As compared with bulk ZnS crystals, ZnS nanoparticles can adsorb more water molecules per unit surface area due to the greatly increased curvature, which increases the distance between adjacent adsorbed molecules. Results from both TPD and MD show that the water binding energy increases with decreasing the water surface coverage. We attribute the increase in binding energy with decreasing surface water coverage to the increasing degree of surface under-coordination as removal of water molecules proceeds. MD also suggests that the water binding energy increases with decreasing particle size due to the further distance and hence lower interaction between adsorbed water molecules on highly curved smaller particle surfaces. Results also show that the binding energy, and thus the strength of interaction of water, is highest in isolated nanoparticles, lower in nanoparticle aggregates, and lowest in bulk crystals. Given that water binding is driven by surface energy reduction, we attribute the decreased binding energy for aggregated as compared to isolated particles to the decrease in surface energy that occurs as the result of inter-particle interactions.

Structure and dynamics of the hydration shells of the Al3+ ion.

First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300 degrees C. The predicted six water molecules in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen bonds to 12 s shell water molecules in agreement with the putative structure used to analyze the x-ray data, but in disagreement with the results reported from conventional molecular dynamics using two-and three-body potentials. Bond lengths and angles of the water molecules in the first and second hydration shells and the average radii of these shells also agreed very well with the results of the x-ray analysis. Water transfers into and out of the second solvation shell were observed to occur on a picosecond time scale via a dissociative mechanism. Beyond the second shell the bonding pattern substantially returned to the tetrahedral structure of bulk water. Most of the simulations were done with 64 solvating water molecules (20 ps). Limited simulations with 128 water molecules (7 ps) were also carried out. Results agreed as to the general structure of the solvation region and were essentially the same for the first and second shell. However, there were differences in hydrogen bonding and Al-O radial distribution function in the region just beyond the second shell. At the end of the second shell a nearly zero minimum in the Al-O radial distribution was found for the 128 water system. This minimum is less pronounced minimum found for the 64 water system, which may indicate that sizes larger than 64 may be required to reliably predict behavior in this region.

Calculation of water-exchange rates on aqueous polynuclear clusters and at oxide-water interfaces.

The rates of a wide variety of reactions in aqueous coordination compounds can be correlated with lifetimes of water molecules in the inner-coordination shell of the metal. For simple octahedral metal ions, these lifetimes span approximately 1020 but are unknown, and experimentally inaccessible, for reactive sites in interfacial environments. Using recent data on nanometer-sized aqueous aluminum clusters, we show that lifetimes can be calculated from reactive-flux molecular dynamics simulations. Rates scale with the calculated metal-water bond lengths. Surprisingly, on all aluminum(III) mineral surface sites investigated, waters have lifetimes in the range of 10-8-10-10 s, making the surface sites as fast as the most reactive ions in the solution.