Dissolution enables dolomite crystal growth near ambient conditions.

Crystals grow in supersaturated solutions. A mysterious counterexample is dolomite CaMg(CO3)2, a geologically abundant sedimentary mineral that does not readily grow at ambient conditions, not even under highly supersaturated solutions. Using atomistic simulations, we show that dolomite initially precipitates a cation-disordered surface, where high surface strains inhibit further crystal growth. However, mild undersaturation will preferentially dissolve these disordered regions, enabling increased order upon reprecipitation. Our simulations predict that frequent cycling of a solution between supersaturation and undersaturation can accelerate dolomite growth by up to seven orders of magnitude. We validated our theory with in situ liquid cell transmission electron microscopy, directly observing bulk dolomite growth after pulses of dissolution. This mechanism explains why modern dolomite is primarily found in natural environments with pH or salinity fluctuations. More generally, it reveals that the growth and ripening of defect-free crystals can be facilitated by deliberate periods of mild dissolution.

Exploring the kinetics of actinyl-EDTA reduction by ferrous iron using quantum-mechanical calculations.

The reduction of An(vi) (An = U, Np, and Pu) to An(iv) significantly decreases its solubility and mobility. This reaction can be hindered by complexation with inorganic (e.g., carbonate) or organic ligands. Ethylenediaminetetraacetic acid (EDTA) is one such organic ligand that forms stable complexes with actinides. Therefore, it may enhance the mobility of actinides. However, the redox kinetics and mechanisms of actinyl (An(v/vi)O2+/2+)-EDTA are not well characterized yet and are thus studied here using quantum-mechanical calculations. The principle is to approach the actinyl-EDTA and Fe2+ (reductant) in small incremental steps and calculate the system energy at each distance. The overall reaction is then delineated into sub-processes (encounter frequency in bulk solution, formation of outer-sphere complex, transition from outer- to inner-sphere complex, and electron transfer), and reaction rates are determined for each sub-process. The formation of outer-sphere complexes occurs rapidly in microseconds to seconds over a wide range of actinyl concentrations (pM to µM); in contrast, the transition to the inner-sphere complex is relatively slow (milliseconds to a few seconds). Immediate electron transfer to form the pentavalent actinide is observed along the reaction path for Np(vi) and Pu(vi), but not for U(vi). Surprisingly, in acidic conditions, one of the carboxylic groups gets protonated in EDTA of [UO2(edta)]2- rather than one of the amino groups. This process-based series of calculations can be applied to any redox reaction and allows the prediction of changes to the rate law and rate-limiting step in a more fundamental way for different environments.

The basis for reevaluating the reactivity of pyrite surfaces: spin states and crystal field d-orbital splitting energies of bulk, terrace, edge, and corner Fe(ii) ions.

Pyrite, one of the most important minerals to catalyze redox reactions in nature and a bulk low-spin Fe mineral, needs to provide high-spin Fe on surfaces to moderate spin-forbidden transitions. Here, the spin state of pyrite is investigated using density functional theory (DFT) calculations on cluster and periodic models. The energies of clusters FexS2x (where x = 4, 8, 16, and 32) were calculated as a function of total spin and different up/down spin configurations. The undercoordinated Fe on surfaces, edges, and corners were found to provide intermediate and high-spin Fe necessary for catalysis. Generally, the lower the crystal field splitting energy (CFSE), Δ, for a particular Fe atom, the higher is the spin density. Pyrite bulk (3D) and surfaces (2D) (+ water to mimic aqueous systems) were examined. The calculated bulk band gap (0.95 eV) is in excellent agreement with previous reports. For the surface, a conducting state is predicted. The calculated CFSE for bulk Fe(ii) in pyrite (∼2.2 eV) agrees with previous CFT results; due to surface states, this CFSE decreases to ∼1 eV on terraces. This study highlights the importance of accurately describing the spin state of pyrite.

Mechanistic Study of Wettability Changes on Calcite by Molecules Containing a Polar Hydroxyl Functional Group and Nonpolar Benzene Rings.

Oil extraction efficiency strongly depends on the wettability status (oil- vs water-wet) of reservoir rocks during oil recovery. Aromatic compounds with polar functional groups in crude oil have a significant influence on binding hydrophobic molecules to mineral surfaces. Most of these compounds are in the asphaltene fraction of crude oil. This study focuses on the hydroxyl functional group, an identified functional group in asphaltenes, to understand how the interactions between hydroxyl groups in asphaltenes and mineral surfaces begin. Phenol and 1-naphthol are used as asphaltene surrogates to model the simplest version of asphaltenes. Adsorption of oil molecules on the calcite {101̅4} surface is described using static quantum-mechanical density functional theory (DFT) calculations and classical molecular dynamics (MD) simulations. DFT calculations indicate that adsorption of phenol and 1-naphthol occurs preferentially between their hydroxyl group and calcite step edges. 1-Naphthol adsorbs more strongly than phenol, with different adsorption geometries due to the larger hydrophobic part of 1-naphthol. MD simulations show that phenol can behave as an agent to separate oil from the water phase and to bind the oil phase to the calcite surface in the water/oil mixture. In the presence of phenol, partial separation of water/oil with an incomplete lining of phenol at the water/oil boundary is observed after 0.2 ns. After 1 ns, perfect separation of water/oil with a complete lining of phenol at the water/oil boundary is observed, and the calcite surface becomes oil-wet. Phenol molecules enclose decane molecules at the water-decane boundary preventing water from repelling decane molecules from the calcite surface and facilitate further accumulation of hydrocarbons near the surface, rendering the surface oil-wet. This study indicates phenol and 1-naphthol to be good proxies for polar components in oil, and they can be used in designing further experiments to test pH, salinity, and temperature dependence to improve oil recovery.

Electrochemical and Spectroscopic Evidence on the One-Electron Reduction of U(VI) to U(V) on Magnetite.

Reduction of U(VI) to U(IV) on mineral surfaces is often considered a one-step two-electron process. However, stabilized U(V), with no evidence of U(IV), found in recent studies indicates U(VI) can undergo a one-electron reduction to U(V) without further progression to U(IV). We investigated reduction pathways of uranium by reducing U(VI) electrochemically on a magnetite electrode at pH 3.4. Cyclic voltammetry confirms the one-electron reduction of U(VI) to U(V). Formation of nanosize uranium precipitates on the magnetite surface at reducing potentials and dissolution of the solids at oxidizing potentials are observed by in situ electrochemical atomic force microscopy. XPS analysis of the magnetite electrodes polarized in uranium solutions at voltages from -0.1 to -0.9 V (E(0)(U(VI)/U(V))= -0.135 V vs Ag/AgCl) show the presence of only U(V) and U(VI). The sample with the highest U(V)/U(VI) ratio was prepared at -0.7 V, where the longest average U-O(axial) distance of 2.05 ± 0.01 Å was evident in the same sample revealed by extended X-ray absorption fine structure analysis. The results demonstrate that the electrochemical reduction of U(VI) on magnetite only yields U(V), even at a potential of -0.9 V, which favors the one-electron reduction mechanism. U(V) does not disproportionate but stabilizes on magnetite through precipitation of mixed-valence state U(V)/U(VI) solids.

Average structure and local configuration of excess oxygen in UO(2+x).

Determination of the local configuration of interacting defects in a crystalline, periodic solid is problematic because defects typically do not have a long-range periodicity. Uranium dioxide, the primary fuel for fission reactors, exists in hyperstoichiometric form, UO(2+x). Those excess oxygen atoms occur as interstitial defects, and these defects are not random but rather partially ordered. The widely-accepted model to date, the Willis cluster based on neutron diffraction, cannot be reconciled with the first-principles molecular dynamics simulations present here. We demonstrate that the Willis cluster is a fair representation of the numerical ratio of different interstitial O atoms; however, the model does not represent the actual local configuration. The simulations show that the average structure of UO(2+x) involves a combination of defect structures including split di-interstitial, di-interstitial, mono-interstitial, and the Willis cluster, and the latter is a transition state that provides for the fast diffusion of the defect cluster. The results provide new insights in differentiating the average structure from the local configuration of defects in a solid and the transport properties of UO(2+x).

Three new silver uranyl diphosphonates: structures and properties.

The hydrothermal reaction of uranium trioxide and methylenediphosphonic acid in the presence of silver nitrate resulted in the formation of three new uranyl coordination polymers: AgUO2[CH2(PO3)(PO3H)] (Ag-1), [Ag2(H2O)1.5]{(UO2)2[CH2(PO3)2]F2}·(H2O)0.5 (Ag-2), and Ag2UO2[CH2(PO3)2] (Ag-3). All consist of uranyl pentagonal bipyramids that form two-dimensional layered structures. Ag-1 and Ag-3 possess the same structural building unit, but the structures are different; Ag-3 is formed through edge-sharing of F atoms to form UO5F2 dimers. The pH and silver cation have significant effects on the structure that is synthesized. Raman spectra of single crystals of Ag-1, Ag-2, and Ag-3 reveal v1 UO2(2+) symmetric stretches of 816 and 829, 822, and 802 cm(-1), respectively. Electronic structure calculations were performed using the projector augmented wave (PAW) method with density functional theory (DFT) to gain insight into the nature of bonding and electronic characteristics of the synthesized compounds. Herein, we report the syntheses, crystal structures, Raman spectroscopy, and luminescent behavior of these three compounds.

Multi-scale simulation of structural heterogeneity of swift-heavy ion tracks in complex oxides.

Tracks formed by swift-heavy ion irradiation, 2.2 GeV Au, of isometric Gd2Ti2O7 pyrochlore and orthorhombic Gd2TiO5 were modeled using the thermal-spike model combined with a molecular-dynamics simulation. The thermal-spike model was used to calculate the energy dissipation over time and space. Using the time, space, and energy profile generated from the thermal-spike model, the molecular-dynamics simulations were performed to model the atomic-scale evolution of the tracks. The advantage of the combination of these two methods, which uses the output from the continuum model as an input for the atomistic model, is that it provides a means of simulating the coupling of the electronic and atomic subsystems and provides simultaneously atomic-scale detail of the track structure and morphology. The simulated internal structure of the track consists of an amorphous core and a shell of disordered, but still periodic, domains. For Gd2Ti2O7, the shell region has a disordered pyrochlore with a defect fluorite structure and is relatively thick and heterogeneous with different degrees of disordering. For Gd2TiO5, the disordered region is relatively small as compared with Gd2Ti2O7. In the simulation, 'facets', which are surfaces with definite crystallographic orientations, are apparent around the amorphous core and more evident in Gd2TiO5 along [010] than [001], suggesting an orientational dependence of the radiation response. These results show that track formation is controlled by the coupling of several complex processes, involving different degrees of amorphization, disordering, and dynamic annealing. Each of the processes depends on the mass and energy of the energetic ion, the properties of the material, and its crystallographic orientation with respect to the incident ion beam.

New insights into the chemical and isotopic composition of human-body biominerals. I: Cholesterol gallstones from England and Greece.

We have analyzed gallstones from four patients of Europe and particularly from England (including samples from a mother and a daughter) and Greece. According to the XRD, FTIR, NMR and laser micro-Raman results the studied materials correspond to typical cholesterol monohydrate (ChM). The micro-morphology of cholesterol microcrystals was investigated by means of SEM-EDS. The XRF results revealed that Ca is the dominant non-organic metal in all gallstones (up to ∼1.95wt.%) together with Fe, Cu, Pb and Ni (up to ~19ppm for each metal). Gallstones from England contain additional Mn (up to ~87ppm) and Zn (up to ∼6ppm) while the sample of the mother contains negligible Zn and Mn, compared to that of her daughter, but significant As (~4.5ppm). All cholesterol gallstones examined are well enriched in potentially toxic metals (Pb, as well as Ni in one case) and metalloids (As also in one case) as compared to the global average. The position of Zn, which is a characteristic biometal, in the structure of cholesterol, was investigated by molecular simulation using the Accelrys Materials Studio(®) software. On the basis of IRMS results, all gallstones examined exhibit a very light δ(13)C signature (average δ(13)C ~-24‰ PDB). Gamma-ray spectrometry measurements indicate the presence of (214)Pb and (214)Bi natural radionuclides due to the (238)U series as well as an additional amount of (40)K.

Multiple H2 occupancy of cages of clathrate hydrate under mild conditions.

Experiments were carried out by reacting H(2) gas with N(2) hydrate at a temperature of 243 K and a pressure of 15 MPa. The characterizations of the reaction products indicated that multiple H(2) molecules can be loaded into both large and small cages of structure II clathrate hydrates. The realization of multiple H(2) occupancy of hydrate cages under moderate conditions not only brings new insights into hydrogen clathrates but also refreshes the perspective of clathrate hydrates as hydrogen storage media.

Electronic structure and energetics of tetragonal SrCuO2 and its high-pressure superstructure phase.

First-principles calculations have been used to investigate the electronic structure and energetics of the simple tetragonal SrCuO2 (P4=mmm) and its high-pressure tetragonal superstructure (P4=mmm). Based on the calculations, the high-pressure phase is metastable as compared with the low pressure tetragonal phase, with an energy difference of 0.13 eV per SrCuO2 formula unit. The energy barrier to the transition from the superstructure to the simple tetragonal structure is 0.24 eV at 7 GPa; thus, high temperatures are required to synthesize the latter. Among the possible structural configurations resulting from the partially occupied oxygen site in the superstructure phase, the most stable structure has a space group PN4m2, reduced from that of the simple tetragonal structure P4=mmm. The detailed analysis of the electronic band structures of the simple tetragonal and superstructure phases suggests that the out-of-plane buckling of the O atoms in the superstructure leads to significant decrease in the O p-Cu d orbital overlap, allowing the energy of the system to be lowered, which is necessary for the structural stability. An understanding of the electronic structure and energetics of the high-pressure superstructure phase and its relation to the simple tetragonal phase provides a basis for exploring the physical properties of the infinite layer, high-TC superconductor.

Nanoscale manipulation of the properties of solids at high pressure with relativistic heavy ions.

High-pressure and high-temperature phases show unusual physical and chemical properties, but they are often difficult to 'quench' to ambient conditions. Here, we present a new approach, using bombardment with very high-energy, heavy ions accelerated to relativistic velocities, to stabilize a high-pressure phase. In this case, Gd(2)Zr(2)O(7), pressurized in a diamond-anvil cell up to 40 GPa, was irradiated with 20 GeV xenon or 45 GeV uranium ions, and the (previously unquenchable) cubic high-pressure phase was recovered after release of pressure. Transmission electron microscopy revealed a radiation-induced, nanocrystalline texture. Quantum-mechanical calculations confirm that the surface energy at the nanoscale is the cause of the remarkable stabilization of the high-pressure phase. The combined use of high pressure and high-energy ion irradiation provides a new means for manipulating and stabilizing new materials to ambient conditions that otherwise could not be recovered.

Tuning electronic properties of functionalized polyhedral oligomeric silsesquioxanes: a DFT and TDDFT study.

The structure and electronic properties of polyhedral oligomeric silsesquioxane (POSS) cages functionalized with different organic groups have been studied using density functional theory and time-dependent density functional theory calculations. Accordingly, the POSS-T8 cage is quite rigid upon functionalization and thus provides a means for spatially separating conjugated organic fragments, which is useful for the realization of novel organic molecular architectures for light-emitting diodes. Moreover, electronic properties can be tuned through the choice of functional groups and their positioning on or within the POSS cage. Attaching an electron-donating group, such as 4-carbazolephenyl, to the silicon atom at the corner of the cage raises the HOMO level, while attaching an electron-withdrawing group, such as 4-cyanophenyl, or inserting an inert molecule, such as N(2), into the POSS cage lowers the LUMO level. Frontier orbital analysis indicates that the POSS cage is partially conjugated and serves a role as electron acceptor. Carrier transport rates are discussed in the frame of Marcus' electron hopping theory. On the basis of the calculated reorganization energies, these POSS compounds can be used as carrier transporting or blocking materials, depending on the functionalization. Exciton binding energies strongly depend on the spatial arrangement of frontier orbitals rather than on molecular sizes.

Density functional theory studies of chloroethene adsorption on zerovalent iron.

Adsorption of perchloroethene (PCE), trichloroethene (TCE), and cis-dichloroethene (cis-DCE) on zerovalent iron is investigated using density functional theory (DFT) to evaluate hypotheses concerning the relative reactivity of these compounds on zerovalent iron. Four different chloroethene adsorption modes on the Fe(110) surface were studied using periodic DFT and the generalized gradient approximation (GGA). Of the adsorption sites examined, the atop site, where the chloroethene C==C bond straddles a surface iron atom, was the most energetically favorable site for the adsorption of all three chloroethenes. Electronic structure and property analyses provide an indication of the extent of sp2-sp3 hybridization. The strong hybridization of the pi-bonding orbital between the chloroethene C==C bond and the iron surface suggests that adsorbed chloroethenes are strongly activated on Fe(110) and are likely precursors for subsequent chloroethene dissociation on the Fe surface. When the effect of solvation is indirectly taken into account in the DFT simulations by considering the hydration energies of chloroethenes in bulkwater,the ordering ofthe adsorption energies of chloroethenes from the aqueous phase onto Fe(110) is in agreement with experimental observation (PCE > TCE > cis-DCE). Electronic properties of the adsorbed configurations of chloroethenes are also presented.

Identification of peptides with targeted adhesion to bone-like mineral via phage display and computational modeling.

The challenges in engineering bone scaffolds reflect the complexity of bone as an organ. The organic-inorganic hybrid system design aims to provide signals within a conductive apatite layer to promote cell adhesion, proliferation and ultimately differentiation into bone tissue. Dual functioning peptides designed to specifically adhere to the apatite layer, while promoting cell adhesion via cell recognition sequences, may increase cell adhesion, leading to increased osteogenesis. The aim of this study is to identify peptide sequences with preferential adsorption towards apatite-based materials. Bone-like mineral films and hydroxyapatite disks were panned with a phage library to elucidate peptide sequences with favorable adsorption. Peptide sequences were analyzed using the web-based biotechnology tool RELIC and validated with a modified ELISA, in addition to being investigated using a newly developed method of high-throughput computational modeling. Peptides having the highest affinity and greatest potential to be incorporated into a dual functioning peptide design are APWHLSSQYSRT, VTKHLNQISQSY and STLPIPHEFSRE. These experiments provide a method of rationally designing peptides that adhere to apatite and that may improve bone tissue regeneration. This work also provides structure for investigating peptide/protein adsorption on apatite substrates with varied carbonate, or other impurity, content.

Pressure-induced splitting and buckling of Cu-O chains in the low-dimensional structure of SrCuO2.

A pressure-induced splitting of the Cu-O chains was found in SrCuO2 at pressures >7 GPa and room temperature. The high-pressure phase is a superstructure of the infinite-layered tetragonal superconducting phase of SrCuO2 and is not stable under ambient conditions. The Cu-O chains buckle with further increasing pressure, and a new high-density polymorph of SrCuO2 is formed at 34.2 GPa.

Expect the unexpected: malposition of a large-bore central venous catheter in the urinary bladder.

We report the case of a femoral vein cannulation in a critically ill trauma patient with the malposition of a large-bore central venous catheter in the urinary bladder. Recognition of the malposition was hampered by bloody tamponade of the bladder in the context of blunt thoraco-abdominal trauma with kidney and liver laceration. A high index of clinical suspicion and the institution of adequate therapy were the key to achieving a successful clinical outcome. We discuss the anatomy of femoral veins, including their close relation to a distended bladder. The application of ultrasound even in emergency situations is stressed.