Stability and Speciation of Hydrated Magnetite {111} Surfaces from Ab Initio Simulations with Relevance for Geochemical Redox Processes.

Magnetite is a common mixed Fe(II,III) iron oxide in mineral deposits and the product of (anaerobic) iron corrosion. In various Earth systems, magnetite surfaces participate in surface-mediated redox reactions. The reactivity and redox properties of the magnetite surface depend on the surface speciation, which varies with environmental conditions. In this study, Kohn-Sham density functional theory (DFT + U method) was used to examine the stability and speciation of the prevalent magnetite crystal face {111} in a wide range of pH and Eh conditions. The simulations reveal that the oxidation state and speciation of the surface depend strongly on imposed redox conditions and, in general, may differ from those of the bulk state. Corresponding predominant phase diagrams for the surface speciation and structure were calculated from first principles. Furthermore, classical molecular dynamics simulations were conducted investigating the mobility of water near the magnetite surface. The obtained knowledge of the surface structure and oxidation state of iron is essential for modeling retention of redox-sensitive nuclides.

Iron Adsorption on Clays Inferred from Atomistic Simulations and X-ray Absorption Spectroscopy.

The atomistic level understanding of iron speciation and the probable oxidative behavior of iron (Feaq2+ → Fesurf3+) in clay minerals are fundamental for environmental geochemistry of redox reactions. Thermodynamic analyses of wet chemistry data suggest that iron adsorbs on the edge surfaces of clay minerals at distinct structural sites commonly referred as strong and weak sites (with high and low affinity, respectively). In this study, we applied ab initio molecular dynamics simulation to investigate the structure and the stability of the edge surfaces of trans- and cis-vacant montmorillonites. These structures were further used to evaluate the surface complexation energy and to calculate reference ab initio X-ray absorption spectra (XAS) for distinct inner-sphere complexes of iron. The combination of ab initio simulations and XAS allowed us to reveal the Fe-complexation mechanism and to quantify the Fe partitioning between the high and low affinity sites as a function of the oxidation state and loadings. Although iron is mostly present in the Fe3+ form, Fe2+ increasingly co-adsorbs at increasing loadings. Ab initio structure relaxations of several different clay structures with substituted Fe2+/Fe3+ in the bulk or at the surface site showed that the oxidative sorption of ferrous iron is an energetically favored process at several edge surfaces of the Fe-bearing montmorillonite.

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations.

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

Characterization of Structural Iron in Smectites - An Ab Initio Based X-ray Absorption Spectroscopy Study.

Fe-bearing clay minerals are abundant in argillaceous rocks as their redox-active structural iron may control the sorption mechanism of redox sensitive elements on the surface of clay minerals. The extent and efficiency of the redox reactions depend on the oxidation state (Fe2+/Fe3+ ratio) and structural distribution of the substituting cations in the TOT-layer of clay minerals. Even smectites with similar structure originating from different locations might have a distinct arrangement of isomorphic substitutions (e.g., individual iron or Fe-Fe pairs). In this study, the proportion of different iron distribution in Milos-, Wyoming-, and Texas-montmorillonite was determined by combining X-ray absorption spectroscopy (XAS) with ab initio calculations. The relaxed atomic structures of the smectite models with different arrangement of individual Fe atoms and Fe-Fe/Fe-Mg clusters served as the basis for the calculations of the XAS spectra. The combination of simulation results and measured Fe K-edge XAS spectra of Wyoming-, Milos- and Texas-montmorillonites suggested that iron is present as Fe3+ in the octahedral sheet. Fe3+ in Texas-montmorillonite has a tendency to form clusters, while no definitive statement about clustering or avoidance of Fe-Fe and Fe-Mg pairs can be made for Milos- and Wyoming-montmorillonite.

Impact of finite-temperature and condensed-phase effects on theoretical X-ray absorption spectra of transition metal complexes.

The impact of condensed-phase and finite-temperature effects on the theoretical X-ray absorption spectra of transition metal complexes is assessed. The former are included in terms of the all-electron Gaussian and augmented plane-wave approach, whereas the latter are taken into account by extensive ensemble averaging along second-generation Car-Parrinello ab initio molecular dynamics trajectories. We find that employing the periodic boundary conditions and including finite-temperature effects systematically improves the agreement between our simulated X-ray absorption spectra and experimental measurements. © 2018 Wiley Periodicals, Inc.

Combined XAFS Spectroscopy and Ab Initio Study on the Characterization of Iron Incorporation by Montmorillonite.

Iron occurs in clay minerals in both ferric and ferrous forms. Depending on its oxidation state and the environmental conditions, it can participate in redox reactions and influence the sorption processes at surfaces of clay minerals. Knowing the oxidation state and the preferential structural position of Fe2+ and Fe3+ is essential for the detailed understanding of the mechanism and kinetics of such processes. In this study, molecular dynamics (MD) calculations based on density functional theory (DFT+U) were applied to simulate the incorporated Fe in bulk montmorillonite and to explain the measured Fe K-edge X-ray absorption fine structure (XAFS) spectra. The analysis of the experimental data and simulation results suggested that iron in montmorillonite is preferentially incorporated as Fe3+ into the octahedral layer. The simulations showed that there is no preferential occupation of cis- or trans-sites by Fe2+ and Fe3+ in bulk montmorillonite. A very good agreement between the ab initio simulated and the measured XAFS spectra demonstrate the robustness of the employed simulation approach.

Prebiotic NH3 Formation: Insights from Simulations.

Simulations of prebiotic NH3 synthesis from NO3⁻ and NO2⁻ on pyrite surfaces under hydrothermal conditions are reported. Ab initio metadynamics calculations have successfully explored the full reaction path which explains earlier experimental observations. We have found that the reaction mechanism can be constructed from stepwise single atom transfers which are compatible with the expected reaction time scales. The roles of the hot-pressurized water and of the pyrite surfaces have been addressed. The mechanistic picture that emerged from the simulations strengthens the theory of chemoautotrophic origin of life by providing plausible reaction pathways for the formation of ammonia within the iron-sulfur-world scenario.

Pyrite in contact with supercritical water: the desolation of steam.

The supercritical water-pyrite interface has been studied by ab initio molecular dynamics simulation. Extreme conditions are relevant in the iron-sulfur world (ISW) theory where prebiotic chemical reactions are postulated to occur at the mineral-water interface. We have investigated the properties of this interface under such conditions. We have come to the conclusion that hot-pressurized water on pyrite leads to an interface where a dry pyrite surface is in contact with the nearby SC water without significant chemical interactions. This picture is markedly different from that under ambient conditions where the surface is fully covered with adsorbed water molecules which is of relevance for the surface reactions of the ISW hypothesis.

Cobalt-free layered perovskites RBaCuFeO5+δ (R = 4f lanthanide) as electrocatalysts for the oxygen evolution reaction.

Co-based perovskite oxides are intensively studied as promising catalysts for electrochemical water splitting in an alkaline environment. However, the increasing Co demand by the battery industry is pushing the search for Co-free alternatives. Here we report a systematic study of the Co-free layered perovskite family RBaCuFeO5+δ (R = 4f lanthanide), where we uncover the existence of clear correlations between electrochemical properties and several physicochemical descriptors. Using a combination of advanced neutron and X-ray synchrotron techniques with ab initio DFT calculations we demonstrate and rationalize the positive impact of a large R ionic radius in their oxygen evolution reaction (OER) activity. We also reveal that, in these materials, Fe3+ is the transition metal cation the most prone to donate electrons. We also show that similar R3+/Ba2+ ionic radii favor the incorporation and mobility of oxygen in the layered perovskite structure and increase the number of available O diffusion paths, which have an additional, positive impact on both, the electric conductivity and the OER process. An unexpected result is the observation of a clear surface reconstruction exclusively in oxygen-rich samples (δ > 0), a fact that could be related to their superior OER activity. The encouraging intrinsic OER values obtained for the most active electrocatalyst (LaBaCuFeO5.49), together with the possibility of industrially producing this material in nanocrystalline form should inspire the design of other Co-free oxide catalysts with optimal properties for electrochemical water splitting.

Study of High-Temperature Behaviour of ZnO by Ab Initio Molecular Dynamics Simulations and X-ray Absorption Spectroscopy.

Wurtzite-type zinc oxide (w-ZnO) is a widely used material with a pronounced structural anisotropy along the c axis, which affects its lattice dynamics and represents a difficulty for its accurate description using classical models of interatomic interactions. In this study, ab initio molecular dynamics (AIMD) was employed to simulate a bulk w-ZnO phase in the NpT ensemble in the high-temperature range from 300 K to 1200 K. The results of the simulations were validated by comparison with the experimental Zn K-edge extended X-ray absorption fine structure (EXAFS) spectra and known diffraction data. AIMD NpT simulations reproduced well the thermal expansion of the lattice, and the pronounced anharmonicity of Zn-O bonding was observed above 600 K. The values of mean-square relative displacements and mean-square displacements for Zn-O and Zn-Zn atom pairs were obtained as a function of interatomic distance and temperature. They were used to calculate the characteristic Einstein temperatures. The temperature dependences of the O-Zn-O and Zn-O-Zn bond angle distributions were also determined.

Interfacial water: a first principles molecular dynamics study of a nanoscale water film on salt.

Density functional theory (DFT) molecular dynamics simulations of a thin (approximately 15 A) water film on NaCl(001) have been performed, with the aim of understanding the structural and dynamic properties of this important interfacial water system. The interaction of the water film with the surface orders the water molecules in the immediate vicinity of the interface. This is reflected by oscillations in the planar-averaged water density distribution along the surface normal that extend to about 8 A from the surface. The interaction with the substrate leaves many of the water molecules in the immediate vicinity with broken hydrogen bonds and as a consequence considerably reduced dipole moments. Indeed a clear correlation between the number of hydrogen bonds which a water molecule is involved in and its dipole moment for both water on NaCl and bulk water is observed. How the DFT results obtained here compare to those obtained with various empirical potentials is briefly discussed.

Density oscillations in a nanoscale water film on salt: insight from ab initio molecular dynamics.

The salt-water interface is one of the most important and common on earth, playing a prominent role in disciplines such as atmospheric science and biology. Despite the apparent simplicity of such interfaces, arguably the most fundamental question of what the nature and structure of the liquid water/salt interface is under ambient conditions remains unclear. Here we address this issue with an ab initio molecular dynamics simulation of a nanoscale liquid water film on NaCl. A pronounced layering is observed in the film, with the density exhibiting a damped oscillatory behavior in the direction of the surface normal. In addition, water molecules in the contact layer are preferentially adsorbed at specific adsorption sites, involved in about 20% fewer hydrogen bonds with each other, and carry considerably reduced dipole moments compared to bulk liquid water.

The Effect of Excess Electron and hole on CO2 Adsorption and Activation on Rutile (110) surface.

CO2 capture and conversion into useful chemical fuel attracts great attention from many different fields. In the reduction process, excess electron is of key importance as it participates in the reaction, thus it is essential to know whether the excess electrons or holes affect the CO2 conversion. Here, the first-principles calculations were carried out to explore the role of excess electron on adsorption and activation of CO2 on rutile (110) surface. The calculated results demonstrate that CO2 can be activated as CO2 anions or CO2 cation when the system contains excess electrons and holes. The electronic structure of the activated CO2 is greatly changed, and the lowest unoccupied molecular orbital of CO2 can be even lower than the conduction band minimum of TiO2, which greatly facilities the CO2 reduction. Meanwhile, the dissociation process of CO2 undergoes an activated CO2(-) anion in bend configuration rather than the linear, while the long crossing distance of proton transfer greatly hinders the photocatalytic reduction of CO2 on the rutile (110) surface. These results show the importance of the excess electrons on the CO2 reduction process.

Effects of stoichiometry on the defect clustering in uranium dioxide.

This study addresses the on-going topic of point defects and point defect clusters in uranium dioxide. Molecular statics simulation using an extended pair potential model that accounts for disproportionation equilibrium as charge compensation has been applied to assess the effect of disproportionation on structural properties and clustering in non-stoichiometric uranium dioxide. The defective structures are scanned in minute detail using a powerful and versatile analysing tool, called ASTRAM, developed in-house for the purpose. Unlike pair potential models ignoring disproportionation effects, our model reproduces volume changes observed experimentally in non-stoichiometric UO2-x and UO2+x. The oxygen defect energetics computed is in good agreement with data in the literature. The model is used to assess the clustering that occurs in bulk samples of non-stoichiometric uranium dioxide. This study confirms the generation of split-interstitial clusters as the dominant defect type in non-stoichiometric uranium dioxide. A new key mechanism for defect clustering in hyper-stoichiometric uranium dioxide is proposed that is based on the progressive aggregation of primitive blocks identified as 1-vacancy split-interstitial clusters.

CO2 Capture and Conversion on Rutile TiO2(110) in the Water Environment: Insight by First-Principles Calculations.

The conversion of CO2 by the virtue of sunlight has the great potential to produce useful fuels or valuable chemicals while decreasing CO2 emission from the traditional fossil fuels. Here, we use the first-principles calculations combined with the periodic continuum solvation model (PCSM) to explore the adsorption and reactivity of CO2 on rutile TiO2(110) in the water environment. The results exhibit that both adsorption structures and reactivity of CO2 are greatly affected by water coadsorption on rutile TiO2(110). In particular, the solvation effect can change the most stable adsorption configuration of CO2 and H2O on rutile TiO2(110). In addition, the detailed conversion mechanism of CO2 reduction is further explored in the water environment. The results reveal that the solvation effect cannot only greatly decrease the energy barrier of CO2 reduction but also affect the selectivity of the reaction processes. These results presented here show the importance of the aqueous solution, which should be helpful to understand the detailed reaction processes of photocatalysts.

Static and Dynamical Properties of Liquid Water from First Principles by a Novel Car-Parrinello-like Approach.

Using the recently developed Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics ( Kühne, T. D. ; et al. Phys. Rev. Lett. 2007 , 98 , 066401. ), we assess the accuracy of ab initio molecular dynamics at the semilocal density functional level of theory to describe structural and dynamic properties of liquid water at ambient conditions. We have performed a series of large-scale simulations using a number of parameter-free exchange and correlation functionals, to minimize and investigate the influence of finite size effects as well as statistical errors. We find that finite size effects in structural properties are rather small and, given an extensive sampling, reproducible. On the other hand, the influence of finite size effects on dynamical properties are much larger than generally appreciated. So much so that the infinite size limit is practically out of reach. However, using a finite size scaling procedure, thanks to the greater effectiveness of our new method we can estimate both the thermodynamic value of the diffusion coefficient and the shear viscosity. The hydrogen bond network structure and its kinetics are consistent with the conventional view of tetrahedrally coordinated water.

Superionic conduction in substoichiometric LiAl alloy: an ab initio study.

Based on the new ab initio molecular dynamics method by Kühne et al. [Phys. Rev. Lett. 98, 066401 (2007)10.1103/PhysRevLett.98.066401], we studied the mechanism of superionic conduction in substoichiometric Li-poor Li_{1+x}Al alloys by performing simulations at different temperatures for an overall simulation time of about 1 ns. The dynamical simulations revealed the microscopic path for the diffusion of Li vacancies. The calculated activation energy (0.11 eV) and the prefactor (D_{0} = 6.9 x 10;{-4} cm;{2}/s) for Li diffusivity via a vacancy-mediated mechanism are in good agreement with experimental NMR data. The calculation of the formation energies of different defects-Li and Al Frenkel pair and Li antisites-revealed that only Li;{+} vacancies and Li_{Al} antisites are present in the stability range of the Zintl phase -0.1 < x < 0.2.

Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics.

We present a new method which combines Car-Parrinello and Born-Oppenheimer molecular dynamics in order to accelerate density functional theory based ab initio simulations. Depending on the system a gain in efficiency of 1 to 2 orders of magnitude has been observed, which allows ab initio molecular dynamics of much larger time and length scales than previously thought feasible. It will be demonstrated that the dynamics is correctly reproduced and that high accuracy can be maintained throughout for systems ranging from insulators to semiconductors and even to metals in condensed phases. This development considerably extends the scope of ab initio simulations.

Simulating fluid-phase equilibria of water from first principles.

Efficient Monte Carlo algorithms and a mixed-basis set electronic structure program were used to compute from first principles the vapor-liquid coexistence curve of water. A water representation based on the Becke-Lee-Yang-Parr exchange and correlation functionals yields a saturated liquid density of 900 kg/m3 at 323 K and normal boiling and critical temperatures of 350 and 550 K, respectively. An analysis of the structural and electronic properties of the saturated liquid phase shows an increase of the asymmetry of the local hydrogen-bonded structure despite the persistence of a 4-fold coordination and decreases of the molecular dipole moment and of the spread of the lowest unoccupied molecular orbital with increasing temperature.