An open database of computed bulk ternary transition metal dichalcogenides

We present a dataset of structural relaxations of bulk ternary transition metal dichalcogenides (TMDs) computed via plane-wave density functional theory (DFT). We examined combinations of up to two chalcogenides with seven transition metals from groups 4-6 in octahedral (1T) or trigonal prismatic (2H) coordination. The full dataset consists of 672 unique stoichiometries, with a total of 50,337 individual configurations generated during structural relaxation. Our motivations for building this dataset are (1) to develop a training set for the generation of machine and deep learning models and (2) to obtain structural minima over a range of stoichiometries to support future electronic analyses. We provide the dataset as individual VASP xml files as well as all configurations encountered during relaxations collated into an ASE database with the corresponding total energy and atomic forces. In this report, we discuss the dataset in more detail and highlight interesting structural and electronic features of the relaxed structures.

Local density changes and carbonate rotation enable Ba incorporation in amorphous calcium carbonate

Incorporation of a Ba impurity in amorphous calcium carbonate (ACC) is shown with ab initio molecular dynamics simulations to have a long-range effect on its atomic-level structure and to be energetically favoured relative to incorporation in crystalline calcium carbonate polymorphs. The ability of carbonate ions to rotate and of ACC to undergo local density changes explain ACC's propensity for incorporating divalent metal impurities with a wide range of ionic radii. These findings provide an atomic-level basis for understanding the significant effects of low concentrations of impurities on the structure of ACC.

Disordered interfaces of alkaline aluminate salt hydrates provide glimpses of Al3+ coordination changes

HYPOTHESIS

The precipitation and dissolution of aluminum-bearing mineral phases in aqueous systems often proceed via changes in both aluminum coordination number and connectivity, complicating molecular-scale interpretation of the transformation mechanism. Here, the thermally induced transformation of crystalline sodium aluminum salt hydrate, a phase comprised of monomeric octahedrally coordinated aluminate which is of relevance to industrial aluminum processing, has been studied. Because intermediate aluminum coordination states during melting have not previously been detected, it is hypothesized that the transition to lower coordinated aluminum ions occurs within ahighly disordered quasi-two-dimensional phase at the solid-solution interface.

EXPERIMENTS AND SIMULATIONS

In situ X-ray diffraction (XRD), Raman and²⁷Al nuclear magnetic resonance (NMR) spectroscopy were used to monitor the melting transition of nonasodium aluminate hydrate (NSA, Na₉[Al(OH)₆]₂·3(OH)·6H₂O). A mechanistic interpretation was developed based on complementary classical molecular dynamics (CMD) simulations including enhanced sampling. A reactive forcefield was developed to bridge speciation in the solution and in the solid phase.

FINDINGS

In contrast to classical dissolution, aluminum coordination change proceeds through a dynamically stabilized ensemble of intermediate states in a disordered layer at the solid-solution interface. In both melting and dissolution of NSA, octahedral, monomeric aluminum transition through an intermediate of pentahedral coordination. The intermediate dehydroxylates to form tetrahedral aluminate (Al(OH)₄^-) in the liquid phase. This coordination change is concomitant with a breaking of the ionic aluminate-sodium ionlinkages. The solution phase Al(OH)₄^- ions subsequently polymerize into polynuclear aluminate ions. However, there are some differences between bulk melting and interfacial dissolution, with the onset of the surface-controlled process occurring at a lower temperature (∼30 °C) and the coordination change taking place more gradually as a function of temperature. This work to determine the local structure and dynamics of aluminum in the disordered layer provides a new basis to understand mechanisms controlling aluminum phase transformations in highly alkaline solutions.

Structural water in amorphous carbonate minerals: ab initio molecular dynamics simulations of X-ray pair distribution experiments

Water is known to play a controlling role in directing mineralization pathways and stabilizing metastable amorphous intermediates in hydrous carbonate mineral MCO₃·nH₂O systems, where M²⁺ is a divalent metal cation. Despite this recognition, the nature of the controls on crystallization is poorly understood, largely owing to the difficulty in characterizing the dynamically disordered structures of amorphous intermediates at the atomic scale. Here, we present a series of atomistic models, derived from ab initio molecular dynamics simulation, across a range of experimentally relevant cations (M = Ca, Mg, Sr) and hydration levels (0 ≤ n ≤ 2). Theoretical simulations of the dependence of the X-ray pair distribution function on the hydration level n show good agreement with available experimental data and thus provide further evidence for a lack of significant nanoscale structure in amorphous carbonates. Upon dehydration, the metal coordination number does not change significantly, but the relative extent of water dissociation increases, indicating that a thermodynamic driving force exists for water dissociation to accompany dehydration. Mg strongly favors monodentate conformation of carbonate ligands and shows a marked preference to exchange monodentate carbonate O for water O upon hydration, whereas Ca and Sr exchange mono- and bidentate carbonate ligands with comparable frequency. Water forms an extensive hydrogen bond network among both water and carbonate groups that exhibits frequent proton transfers for all three cations considered suggesting that proton mobility is likely predominantly due to water dissociation and proton transfer reactions rather than molecular water diffusion.

Theory-Guided Inelastic Neutron Scattering of Crystalline Alkaline Aluminate Salts Bearing Principal Motifs of Solution-State Species

Aluminate salts precipitated from caustic alkaline solutions exhibit a correlation between the anionic speciation and the identity of the alkali cation in the precipitate, with the aluminate ions occurring either in monomeric (Al(OH)₄^-) or dimeric (Al₂O(OH)₆^2-) forms. The origin of this correlation is poorly understood as are the roles that oligomeric aluminate species play in determining the solution structure, prenucleation clusters, and precipitation pathways. Characterization of aluminate solution speciation with vibrational spectroscopy results in spectra that are difficult to interpret because the ions access a diverse and dynamic configurational space. To investigate the Al(OH)₄^- and Al₂O(OH)₆^2- anions within a well-defined crystal lattice, inelastic neutron scattering (INS) and Raman spectroscopic data were collected and simulated by density functional theory for K₂[Al₂O(OH)₆], Rb₂[Al₂O(OH)₆], and Cs[Al(OH) ₄]·2H₂O. These structures capture archetypal solution aluminate species: the first two salts contain dimeric Al₂O(OH)₆^2- anions, while the third contains the monomeric Al(OH)₄^- anion. Comparisons were made to the INS and Raman spectra of sodium aluminate solutions frozen in a glassy state. In contrast to solution systems, the crystal lattice of the salts results in well-defined vibrations and associated resolved bands in the INS spectra. The use of a theory-guided analysis of the INS of this solid alkaline aluminate series revealed that differences were related to the nature of the hydrogen-bonding network and showed that INS is a sensitive probe of the degree of completeness and strength of the bond network in hydrogen-bonded materials. Results suggest that the ionic size may explain cation-specific differences in crystallization pathways in alkaline aluminate salts.

Tuning Electronic Properties of 2D Materials Using Metal Adsorbates: Cu at WTe2 Edges

Two-dimensional materials exhibit properties promising for novel applications. Topologically protected states at their edges can be harnessed for use in quantum devices. We use ab initio simulations to examine properties of edges in 1T'-WTe₂ monolayers, known to exhibit topological order, and their interactions with Cu atoms. Comparison of (010)-oriented edges that have the same composition but different terminations shows that, as the number of Cu atoms increases, their thermodynamically preferred arrangement depends on the details of the edge structure. Cu atoms aggregate into a cluster at the most stable edge; while the cluster is nonmagnetic, it spin-polarizes the W atoms along the edge, which removes the topological protection. At the metastable edge, Cu atoms form a chain incorporated into the WTe₂ lattice; the topological state is preserved in spite of the dramatic edge restructuring. This suggests that exploiting interactions of metal species with metastable edge terminations can provide a path toward noninvasive interfaces.

Inference of principal species in caustic aluminate solutions through solid-state spectroscopic characterization

Tetrahedrally coordinated aluminate Al(OH)₄^- and dialuminate Al₂O(OH)₆^2- anions are considered to be major species in aluminum-rich alkaline solutions. However, their relative abundance remains difficult to spectroscopically quantify due to local structure similarities and poorly understood effects arising from extent of polymerization and counter-cations. To help unravel these relationships here we report detailed characterization of three solid-phase analogues as structurally and compositionally well-defined reference materials. We successfully synthesized a cesium salt of the aluminate monomer, CsAl(OH)₄·2H₂O, for comparison to potassium and rubidium salts of the aluminate dimer, K₂Al₂O(OH)₆, and Rb₂Al₂O(OH)₆, respectively. Single crystal and powder X-ray diffraction methods clearly reveal the structure and purity of these materials for which a combination of ²⁷Al MAS-NMR, Al K-edge X-ray absorption and Raman/IR spectroscopies was then used to fingerprint the two major tetrahedrally coordinated Al species. The resulting insights into the effect of Al-O-Al bridge formation between aluminate tetrahedra on spectroscopic features may also be generalized to the many materials that are based on this motif.

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.

Cr(III) Adsorption by Cluster Formation on Boehmite Nanoplates in Highly Alkaline Solution

The development of advanced functional nanomaterials for selective adsorption in complex chemical environments requires partner studies of binding mechanisms. Motivated by observations of selective Cr(III) adsorption on boehmite nanoplates (γ-AlOOH) in highly caustic multicomponent solutions of nuclear tank waste, here we unravel the adsorption mechanism in molecular detail. We examined Cr(III) adsorption to synthetic boehmite nanoplates in sodium hydroxide solutions up to 3 M, using a combination of X-ray diffraction (XRD), Raman, X-ray photoelectron spectroscopy (XPS), scanning/transmission electron microscopy (S/TEM), electron energy loss spectroscopy (EELS), high-resolution atomic force microscopy (HR-AFM), time-of-fight secondary ion mass spectrometry (ToF-SIMS), Cr K-edge X-ray absorption near edge structure (XANES)/extended X-ray absorption fine structure (EXAFS), and electron paramagnetic resonance (EPR). Adsorption isotherms and kinetics were successfully fit to Langmuir and pseudo-second-order kinetic models, respectively, consistent with monotonic uptake of Cr(OH)₄^- monomers until saturation coverage of approximately half the aluminum surface site density. High resolution AFM revealed monolayer cluster self-assembly on the (010) basal surfaces with increasing Cr(III) loading, possessing a structural motif similar to guyanaite (β-CrOOH), stabilized by corner-sharing Cr-O-Cr bonds and attached to the surface with edge-sharing Cr-O-Al bonds. The selective uptake appears related to short-range surface templating effects, with bridging metal connections likely enabled by hydroxyl anion ligand exchange reactions at the surface. Such a cluster formation mechanism, which stops short of more laterally extensive heteroepitaxy, could be a metal uptake discrimination mechanism more prevalent than currently recognized.

Electronic response of aluminum-bearing minerals

Aluminum-bearing minerals show different hydrogen evolution and dissolution properties when subjected to radiation, but the complicated sequence of events following interaction with high-energy radiation is not understood. To gain insight into the possible mechanisms of hydrogen production in nanoparticulate minerals, we study the electronic response and determine the bandgap energies of three common aluminum-bearing minerals with varying hydrogen content: gibbsite (Al(OH)₃), boehmite (AlOOH), and alumina (Al₂O₃) using electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and first-principles electronic structure calculations employing hybrid density functionals. We find that the amount of hydrogen has only a small effect on the number and spectrum of photoexcitations in this class of materials. Electronic structure calculations demonstrate that low energy electrons are isotropically mobile, while holes in the valence band are likely constrained to move in layers. Furthermore, holes in the valence band of boehmite are found to be significantly more mobile than those in gibbsite, suggesting that the differences in radiolytic and dissolution behavior are related to hole transport.

Simulation of probe position-dependent electron energy-loss fine structure

We present a theoretical framework for calculating probe-position-dependent electron energy-loss near-edge structure for the scanning transmission electron microscope by combining density functional theory with dynamical scattering theory. We show how simpler approaches to calculating near-edge structure fail to include the fundamental physics needed to understand the evolution of near-edge structure as a function of probe position and investigate the dependence of near-edge structure on probe size. It is within this framework that density functional theory should be presented, in order to ensure that variations of near-edge structure are truly due to local electronic structure and how much from the diffraction and focusing of the electron beam.

Simulation of spatially resolved electron energy loss near-edge structure for scanning transmission electron microscopy

Aberration-corrected scanning transmission electron microscopy yields probe-position-dependent energy-loss near-edge structure (ELNES) measurements, potentially providing spatial mapping of the underlying electronic states. ELNES calculations, however, typically describe excitations by a plane wave traveling in vacuum, neglecting the interaction of the electron probe with the local electronic environment as it propagates through the specimen. Here, we report a methodology that combines a full electronic-structure calculation with propagation of a focused beam in a thin film. The results demonstrate that only a detailed calculation using this approach can provide quantitative agreement with observed variations in probe-position-dependent ELNES.

Direct determination of the chemical bonding of individual impurities in graphene

Using a combination of Z-contrast imaging and atomically resolved electron energy-loss spectroscopy on a scanning transmission electron microscope, we show that the chemical bonding of individual impurity atoms can be deduced experimentally. We find that when a Si atom is bonded with four atoms at a double-vacancy site in graphene, Si 3d orbitals contribute significantly to the bonding, resulting in a planar sp(2) d-like hybridization, whereas threefold coordinated Si in graphene adopts the preferred sp(3) hybridization. The conclusions are confirmed by first-principles calculations and demonstrate that chemical bonding of two-dimensional materials can now be explored at the single impurity level.

Observations of Co4+ in a higher spin state and the increase in the Seebeck coefficient of thermoelectric Ca3Co4O9

Ca3Co4O9 has a unique structure that leads to exceptionally high thermoelectric transport. Here we report the achievement of a 27% increase in the room-temperature in-plane Seebeck coefficient of Ca3Co4O9 thin films. We combine aberration-corrected Z-contrast imaging, atomic-column resolved electron energy-loss spectroscopy, and density-functional calculations to show that the increase is caused by stacking faults with Co4+-ions in a higher spin state compared to that of bulk Ca3Co4O9. The higher Seebeck coefficient makes the Ca3Co4O9 system suitable for many high temperature waste-heat-recovery applications.

Atomic structure of highly strained BiFeO3 thin films

We determine the atomic structure of the pseudotetragonal T phase and the pseudorhombohedral R phase in highly strained multiferroic BiFeO(3) thin films by using a combination of atomic-resolution scanning transmission electron microscopy and electron energy-loss spectroscopy. The coordination of the Fe atoms and their displacement relative to the O and Bi positions are assessed by direct imaging. These observations allow us to interpret the electronic structure data derived from electron energy-loss spectroscopy and provide evidence for the giant spontaneous polarization in strained BiFeO(3) thin films.

Reducing radiation damage in macromolecular crystals at synchrotron sources

A new strategy is presented to reduce primary X-ray damage in macromolecular crystallography. The strategy is based on separating the diffracting and damaged regions as much as feasible. The source of the radiation damage to macromolecular crystals is from two primary mechanisms: the direct excitations of electrons by absorption, and inelastic scattering of the X-rays. The first produces photoelectrons with their accompanying Auger electrons from relaxation of the core hole and the second creates Compton electrons. The properties of these two mechanisms and calculations of primary X-ray damage quantify how to modify the spatial distribution of X-rays to reduce the deleterious effects of radiation damage. By focusing the incident X-rays into vertical stripes, it is estimated that the survival (the time during which quality diffraction data can be obtained with a given X-ray flux) of large crystals can be increased by at least a factor of 1.6, while for very small platelet crystals the survival can be increased by up to a factor of 14.