Alfonso Hernández-Laguna

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

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.

Monte Carlo simulations of ordering of Al, Fe, and Mg cations in the octahedral sheet of smectites and illites

Abstract The ordering of Al3+, Fe3+, and Mg2+ cations along the octahedral sheet in dioctahedral 2:1 phyllosilicates was studied theoretically. The distribution of Fe3+/Mg2+ was studied in the octahedral sheet and is compared with the Al3+/Fe3+ and Al3+/Mg2+ distributions. The cation exchange interaction parameters Jn, as first, second, third, and fourth nearest neighbors were calculated by means of empirical interatomic potentials. Several compositions with different interlayer cations, and tetrahedral charge close to ferric smectites, illites, and nontronites were studied. From these Jn values, a trend to form FeMg pairs was observed in the Fe/Mg system. Monte Carlo (MC) simulations based on the previously calculated cation exchange potentials Jn of these systems showed ordering phase transitions in the distribution of the octahedral cations, with different ordering patterns in each case. The two-species model was extended to a three-species ordering MC simulation model. A new procedure to study the ordering of three species is presented in this paper. We present for the first time a theoretical study of the ordering of three octahedral cations Al3+, Fe3+, and Mg2+ in clays, describing compositions more realistic for dioctahedral clay minerals, by means of Monte Carlo simulations based only on atomistic models. Short-range ordering of Fe was found in compositions of smectites and illites reproducing experimental cation distribution patterns.

DFT Research on the Dehydroxylation Reaction of Pyrophyllite 1. First-Principle Molecular Dynamics Simulations

The dehydroxylation of pyrophyllite involves the reaction of OH groups and elimination of water molecules through two possible mechanisms, one involving the bridging hydroxyl groups of an octahedral Al (3+) pair and the other two hydroxyl groups reacting across the dioctahedral vacancy. First-principles molecular dynamics simulations at the density functional theory level are used together with the metadynamics algorithm to explore the free-energy surface (FES) of the initial step of the dehydroxylation. We observe that the two possible dehydroxylation mechanisms yield similar activation energies at 0 K, but at high temperatures, the cross mechanism has lower free energy than that of the on-site one. The dehydroxylation process produces different semidehydroxylated intermediates that should be taken into account. The role of the temperature in favoring a dehydroxylation nonconcerted chain mechanism over another is here elucidated, and a novel competitive mechanism, which is assisted by the structural apical oxygens in the high-temperature regime, is proposed.

Quantum mechanical calculations of trans-vacant and cis-vacant polymorphism in dioctahedral 2:1 phyllosilicates

Abstract Trans-vacant and cis-vacant polymorphs of smectites and illites were distinguished by studying different cation substitutions in octahedral and tetrahedral sheets and in the interlayer. 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. The calculations reproduce the differences in the lattice parameters between the cis-vacant and trans-vacant configurations as observed from experimental studies of phyllosilicates. This theoretical approach is a useful tool for predicting crystallographic properties that must be calculated for smectites and illites because they cannot be determined experimentally in these clay minerals, especially the cis-vacant and trans-vacant configurations. The effect of cation substitutions in the octahedral and tetrahedral sheets on various structural features is also presented. The calculated effects are consistent with experimental results. The energy differences between the cis-vacant and trans-vacant polymorphs for a given composition are lower than the energy changes produced by the relative cation distributions in the octahedral sheet. Nevertheless, in the most illitic samples the trans-vacant arrangement is more stable than the cis-vacant form, in accord with experimental studies.

Quantum mechanical and QSAR study of some α-arylpropionic acids as anti-inflammatory agents

Abstract The optimal structures of a series of α-arylpropionic acids with anti-inflammatory activity are established by using the semi-empirical quantum mechanical procedures, AMI and AMSOL, in the gas phase and in water solution, respectively. In these calculations, the arylpropionic acids are considered in their neutral and ionized forms. As expected, these compounds exhibit two preferred conformations in which the α-hydrogen atoms of the propionic acid group lies approximately in the plane of the central aryl ring. The deprotonation energies are then determined as the difference between the formation energies of the protonated and deprotonated forms. A Quantitative Structure Activity Relationship (QSAR) study reveals that only the gas phase results compare to some extent favorably with the anti-inflammatory activity. As expected, the smaller the deprotonation energy, the larger the anti-inflammatory activity. Satisfactory relationships between the in vivo activities and deprotonation energies, the HOMO energies and lipophilicities were found.

A computational investigation of the Al/Fe/Mg order-disorder behavior in the dioctahedral sheet of phyllosilicates

Abstract In previous papers, we investigated via Monte Carlo simulation the order-disorder behavior of an individual octahedral phyllosilicate sheet, with respect to two-species systems Al/Fe, Al/Mg, and Fe/Mg, and some three-species systems Al/Fe/Mg that were relevant to clay compositions found in nature. We have extended the work on Al/Fe/Mg systems to include a wide range of different octahedral compositions that can represent different natural and synthetic clay minerals, by means of Monte Carlo simulations based only on atomistic models. In many cases, phase transitions do not occur, in that long-range order is not attained, but most systems exhibit short-range order at low temperatures. The ordering of the octahedral cations is highly dependent on the cation composition.

Theoretical study of some H2-receptor agonists of histamine. The H2-essential conformation of histamine

Abstract The conformational energy maps and charge distributions of histamine and six H2-receptor agonists of histamine were determined in the CNDO/2 approach. When several tautomeric forms were possible only the NτH was considered. A judicious analysis of the conformational results, as a function of the H2-receptor activity, allows us to propose, as “essential” for the H2-receptor agonists, an open conformation, trans—trans, for the side chain. The analysis of the relationship between the mean charges on the aromatic ring and the activities supports this conclusion.

Pyrophyllite dehydroxylation process by First Principles calculations

Abstract The crystal structure of triclinic pyrophyllite and its dehydroxylate derivative was studied with quantum mechanical calculations. The standard Kohn-Sham self-consistent density functional theory (DFT) was used through a linear-scaling DFT method with periodical boundary conditions in the generalized gradient approximation (GGA) with numerical atomic orbitals as the basis set. The calculations reproduce the lattice parameters found experimentally in pyrophyllite and its dehydroxylate derivative. The geometrical disposition of the OH bond in the crystal lattice and the hydrogen bonds and other electrostatic interactions of this group were analyzed. The frequencies of different vibration modes were calculated and compared with experimental data; the results show a good agreement. The dehydroxylation process, including different intermediates of this reaction, was investigated theoretically. The energetic differences are according to the thermodynamics of the experimental process. The semidehydroxylate derivative is identified, for the first time, as an important intermediate in this process, clarifying previous questions concerning the mechanism reported from the experimental data.

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.