Vicente Timón

Quantum mechanical calculations of dioctahedral 2:1 phyllosilicates: Effect of octahedral cation distributions in pyrophyllite, illite, and smectite

Abstract The structure of dioctahedral 2:1 phyllosilicates with different interlayer charge was studied theoretically using ab initio calculations. The standard Kohn-Sham self-consistent density functional method was used in the generalized gradient approximation (GGA), with numerical atomic orbitals as the basis set, by means of the SIESTA program. Once the method had been checked satisfactorily, the theoretical study was extended beyond the systems for which there are experimental information, and structural characteristics were predicted. The SIESTA program was shown to be a useful tool in studying the crystallographic properties of 2:1-dioctahedral phyllosilicates. The crystal structures of pyrophyllite, beidellite, and other smectites and illites were simulated. The experimental crystallographic properties of phyllosilicates with high, medium, and low interlayer charge were reproduced. The calculated structures agree with the main experimental structural features of the crystal lattice of these minerals. The effect of cation substitutions in the octahedral and tetrahedral sheets was also studied. The calculated effects are consistent with experimental results. The Mg2+ cations were found to have a tendency to be distributed in the octahedral sheet, in contrast to Fe3+ ions that tend to be clustered

The structure of schwertmannite, a nanocrystalline iron oxyhydroxysulfate

Abstract Schwertmannite is a poorly crystalline mineral that forms ochre rusts and precipitates in acid mine environments. Despite its ubiquity and its role as scavenger of important contaminants such as arsenic or selenium, its structure has not been yet determined. Here, a structure for schwertmannite is presented based on pair distribution function (PDF) data, X-ray diffraction (XRD) analyses, and density functional theory (DFT) calculations. We propose a structure formed by a deformed frame of iron octahedra similar to that of akaganeite. Simulations of X-ray diffraction patterns unveil the presence of long-range order associated with the position of the sulfate molecules, providing a useful way to discern two types of sulfate complexes in the structure. The simulations suggest that two sulfate molecules per unit cell are present in the structure forming one outer sphere and one inner sphere complex inside the channels formed by iron octahedra. Knowledge of the positions of the sulfates in the structure will help to better understand exchange processes with oxyanions of trace contaminants, such as arsenate, chromate, or selenate, that strongly influence their biogeochemical cycling in mining ecosystems.

Isomorphous substitution effect on the vibration frequencies of hydroxyl groups in molecular cluster models of the clay octahedral sheet

Abstract The geometrical features and electronic structure of molecular clusters models of two octahedrally coordinated cations in edge-sharing octahedra were studied by means of Hartree-Fock ab initio molecular orbital calculations at LANL2DZ and 6-31+G* levels. These models represent the different cation pairs among Al3+, Fe3+, and Mg2+ of the octahedral sheet of clays. These models reproduce the experimental values of the main geometrical features in the corresponding minerals. The vibrational frequencies of the bridging hydroxyl groups (M-OH-M’) were calculated and compared with experimental data. A good agreement between theoretical and experimental results was found. The relative differences of ν(OH) and δ(OH) frequencies calculated among these (M-OHM’) cation pairs are similar to the experimental behavior in clays. Theoretical g(OH) frequencies were also calculated and presented as an estimation of the experimental. Correlations between the atomic weights and the atomic Mulliken charges of the cations with the experimental and theoretical OH vibration frequencies have been also determined and a similar behavior was found.

Isomorphous cation substitution in dioctahedral phyllosilicates by means of ab initio quantum mechanical calculations on clusters

Abstract A critical question in radiometric dating of metamorphic rocks is whether minerals used to define internal isochrons have achieved isotopic equilibrium during a given metamorphic event, followed by preservation of the equilibrium afterward. A garnet peridotite at Zhimafang in the Sulu terrane of eastern China shows incongruent U-Pb, Rb-Sr, and Sm-Nd ages. Zircon SHRIMP U-Pb dating yielded an isochron age of 224 ± 8 Ma, pointing to zircon growth during Triassic UHP metamorphism. Two mineral assemblages gave consistent Rb-Sr internal isochron ages of 201 ± 4 and 205 ± 4 Ma, but much older Sm-Nd internal isochron ages of 376 ± 16 and 378 ± 24 Ma. Apparently, the Sm-Nd radiometric system fails to reequilibrate among the dated minerals during the Triassic UHP metamorphic event for the garnet peridotite. This result is confirmed by the state of oxygen isotope equilibrium (or disequilibrium) among the constituent minerals in the garnet peridotite. In particular, garnet is not in oxygen isotope equilibrium with any other of the analyzed minerals. The degree of oxygen isotope disequilibria among the other minerals varies from pair to pair. Oxygen isotope equilibrium is observed only between orthopyroxene and olivine for both samples and between phlogopite and clinopyroxene for one sample. It appears that the U-Pb, Rb-Sr, Sm-Nd, and O isotope systems in minerals of the garnet peridotite are in partial equilibrium during UHP metamorphism, i.e., equilibrium with respect to some isotopes and minerals, but not all. Based on available experimental diffusion data, our study of the combined U-Pb, Rb-Sr, Sm-Nd, and O isotope systems in the garnet peridotite demonstrates that the time scale for the UHP metamorphism and subsequent HP eclogite-facies recrystallization is possibly in the range of about 12 to 26 Ma, which was not long enough for the reequilibration of the Sm-Nd and O isotope systems, but just long enough for the reequilibration of the Rb-Sr isotope systems. Therefore, the rate of Sr diffusion in phlogopite (thus Sr isotope reequilibration between the mafic minerals) is constrained to be faster than rates of Nd and O diffusion in garnet (thus Sm-Nd and O isotope reequilibration between the same minerals) under conditions of subduction zone metamorphism.

High-pressure behavior of 2M1 muscovite

Abstract The crystal structure and pressure influence (between 0-6 GPa) on 2M1 muscovite have been calculated by quantum-mechanical methods based on density functional theory (DFT) with optimized numerical LCAO basis sets and norm-conserving pseudopotentials. Tensions between 0.8 and 0 GPa have been also studied. Volumes as a function of pressure, computed from the generalized gradient approximation, are closer to the experimental data than volumes calculated from the local density approximation. The crystal structure, bond distances, and main geometrical features agree with previous experimental values. A third-order Birch-Murnagham equation is fitted, giving a bulk modulus of 60.1 GPa, which reasonably agrees with the experimental data. Axis compressibilities are slightly smaller than those of the experimental data. The most compressible axis is the c axis. Bond strains, angles, the main geometrical features, and polyhedral strains are studied as a function of pressure, and these vary according to the experimental behavior. Tetrahedral and angles and corrugation show an oscillating behavior in the range of pressures used. The most important compressibilities are those related to the interlayer space, as it corresponds to the weakest bonding in the structure. The highest compressibility in the T-O-T layer along the [001] direction is determined by the octahedral sheet thickness. The compressibilities along the a and b axes are determined by the tetrahedra, as the most compressible polyhedra, and the α angle. Therefore, with our results the utility of periodic DFT methods for studying crystal structure and the effect of hydrostatic pressure on 2M1 muscovite are once again validated, and they are suitable to describe the compression of the crystal structure in detail.

Influence of the alkyl and alkoxy side chains on the electronic structure and charge-transport properties of polythiophene derivatives.

Density Functional Theory has been used to study the structural, electronic and charge-transport properties of two regio-regular head-to-tail polythiophene derivatives, i.e. poly(3-hexyl-thiophene), P3HT, and poly(3-oxyhexyl-thiophene), P3OHT. The effect of substituents on the electronic structure was analyzed by means of bandwidth, bandgap, effective mass, total and partial densities of states and crystal orbital overlap populations. Electronic couplings were estimated from band diagrams as the splitting of the valence band. The neutral and cationic states of isolated oligomers were optimized using the supercell approximation. The hole-transfer rates and mobilities were evaluated according to Marcuss theory. Results provide a compelling illustration of the effect of side chains on the crystal packing, electronic structure and charge-transport properties. Thus, the hole mobility calculated for the alkyl derivative was 0.15 cm(2) V(-1) s(-1) (experimental mobility is 0.10 cm(2) V(-1) s(-1)), while the alkoxy derivative has a theoretical mobility of 0.49 cm(2) V(-1) s(-1). The obtained results hopefully could motivate experimentalists to try out P3OHT for an improved charge carrier mobility.

Vibrations of H+(D+) in stoichiometric LiNbO3 single crystal

A first principles quantum mechanical calculation of the vibrational energy levels and transition frequencies associated with protons in stoichiometric LiNbO(3) single crystal has been carried out. The hydrogen contaminated crystal has been approximated by a model one obtains by translating a supercell, i.e., a cluster of LiNbO(3) unit cells containing a single H(+) and a Li(+) vacancy. Based on the supercell model an approximate Hamiltonian operator describing vibrations of the proton sublattice embedded in the host crystal has been derived. It is further simplified to a sum of uncoupled Hamiltonian operators corresponding to different wave vectors (ks) and each describing vibrations of a quasi-particle (quasi-proton). The three dimensional (3D) Hamiltonian operator of k=0 has been employed to calculate vibrational levels and transition frequencies. The potential energy surface (PES) entering this Hamiltonian operator has been calculated point wise on a large set of grid points by using density functional theory, and an analytical approximation to the PES has been constructed by non-parametric approximation. Then, the nuclear motion Schrödinger equation has been solved by employing the method of discrete variable representation. It has been found that the (quasi-)H(+) vibrates in a strongly anharmonic PES. Its vibrations can be described approximately as a stretching, and two orthogonal bending vibrations. The theoretically calculated transition frequencies agree within 1% with those experimentally determined, and they have allowed the assignment of one of the hitherto unassigned bands as a combination of the stretching and the bending of lower fundamental frequency.

Structure of OH− defects in LiNbO3

The geometry of the most stable configuration of OH− defects in nearly stoichiometric, hydrogen-contaminated, LiNbO3 has been determined from first principles theoretical calculations. In the most stable configuration the proton is located near a bisector of an oxygen triangle and is tilted by 4.3 degrees out of the oxygen plane towards a lithium vacancy. The equilibrium length of the OH− bond has been found to be 0.988 A.

Study of the thermal stability of studtite by in situ Raman spectroscopy and DFT calculations

The design of a safe spent nuclear fuel repository requires the knowledge of the stability of the secondary phases which precipitate when water reaches the fuel surface. Studtite is recognized as one of the secondary phases that play a key-role in the mobilization of the radionuclides contained in the spent fuel. Thereby, it has been identified as a product formed under oxidation conditions at the surface of the fuel, and recently found as a corrosion product in the Fukushima-Daiichi nuclear plant accident. Thermal stability is one of the properties that should be determined due to the high temperature of the fuel. In this work we report a detailed analysis of the structure and thermal stability of studtite. The structure has been studied both by experimental techniques (SEM, TGA, XRD and Raman spectroscopy) and theoretical DFT electronic structure and spectroscopic calculations. The comparison of the results allows us to perform for the first time the Raman bands assignment of the whole spectrum. The thermal stability of studtite has been analyzed by in situ Raman spectroscopy, with the aim of studying the effect of the heating rate and the presence of water. For this purpose, a new cell has been designed. The results show that studtite is stable under dry conditions only at temperatures below 30°C, in contrast with the higher temperatures published up to date (~130°C). Opposite behaviour has been found when studtite is in contact with water; under these conditions studtite is stable up to 90°C, what is consistent with the encounter of this phase after the Fukushima-Daiichi accident.

Plasma generation and processing of interstellar carbonaceous dust analogs

Interstellar (IS) dust analogs, based on amorphous hydrogenated carbon (a-C:H) were generated by plasma deposition in RF discharges of CH4 + He mixtures. The a-C:H samples were characterized by means of secondary electron microscopy (SEM), infrared (IR) spectroscopy and UV-visible reflectivity. DFT calculations of structure and IR spectra were also carried out. From the experimental data, atomic compositions were estimated. Both IR and reflectivity measurements led to similar high proportions (≈ 50%) of H atoms, but there was a significant discrepancy in the sp2/sp3 hybridization ratios of C atoms (sp2/sp3 = 1.5 from IR and 0.25 from reflectivity). Energetic processing of the samples with 5 keV electrons led to a decay of IR aliphatic bands and to a growth of aromatic bands, which is consistent with a dehydrogenation and graphitization of the samples. The decay of the CH aliphatic stretching band at 3.4 µm upon electron irradiation is relatively slow. Estimates based on the absorbed energy and on models of cosmic ray (CR) flux indicate that CR bombardment is not enough to justify the observed disappearance of this band in dense IS clouds.