Claro Ignacio Sainz-Díaz

Computational methods for the study of energies of cation distributions: applications to cation-ordering phase transitions and solid solutions

Abstract The structural and thermodynamic properties of minerals are strongly affected by cation site-ordering processes. We describe methods to determine the main interatomic interactions that drive the ordering process, which are based on parameterizing model Hamiltonians using empirical interatomic potentials and/or ab initio quantum mechanics methods. The methods are illustrated by a number of case study examples, including Al/Si ordering in aluminosilicates, Mg/Ca ordering in garnets, simultaneous Al/Si and Mg/Al ordering in pyroxenes, micas and amphiboles, and Mg/Al non-convergent ordering in spinel using only quantum mechanical methods.

Monte Carlo methods for the study of cation ordering in minerals

Abstract This paper reviews recent applications of Monte Carlo methods for the study of cation ordering in minerals. We describe the program Ossia99, designed for the simulation of complex ordering processes and for use on parallel computers. A number of applications for the study of long-range and short-range order are described, including the use of the Monte Carlo methods to compute quantities measured in an NMR experiment. The method of thermodynamic integration for the determination of the free energy is described in some detail, and several applications of the method to determine the thermodynamics of disordered systems are outlined.

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.

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.

Density functional theory and Monte Carlo study of octahedral cation ordering of Al/Fe/Mg cations in dioctahedral 2:1 phyllosilicates

Abstract The ordering of octahedral Al3+, Fe3+, and Mg2+ cations in dioctahedral 2:1 phyllosilicates was studied theoretically. Quantum mechanical calculations based on density functional theory (DFT) were performed for optimizing different cation distributions along the octahedral sheet. Three systems of two species (Al3+/Mg2+, Al3+/Fe3+, and Fe3+/Mg2+) were studied to obtain the cation exchange potentials Jn as first, second, third, and fourth nearest neighbors. Monte Carlo (MC) simulations based on the previously calculated cation exchange potentials Jn of these binary systems showed ordering phase transition in the distribution of the octahedral cations, with different ordering patterns. Ordered phases are depending on composition and on third and fourth neighbor range interactions. The effect of hydrostatic pressure can affect the cation ordering of the octahedral sheet. The two-species model was extended to a three-species ordering MC simulation model. In our case, we do not find perfect long-range ordering in the three-species systems. Instead we find some domains with different ordering patterns.

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.

Effect of the tetrahedral charge on the order-disorder of the cation distribution in the octahedral sheet of smectites and illites by computational methods

The order-disorder behavior of the isomorphous cation substitution of the octahedral sheet of phyllosilicates was investigated by Monte Carlo simulations based only on atomistic models in some three-species systems Al/Fe/Mg including a wide range of different octahedral compositions that can be relevant to clay compositions found in nature, especially for smectites and illites. 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 temperature. The ordering of the octahedral cations is highly dependent on the cation composition. Variations in the tetrahedral charge (smectite vs. illite) produce slight differences in the cation distribution and the short-range and long-range order of octahedral cations do not change drastically. The average size of Fe clusters and the long-range order of Fe are not larger in illites than in smectites as previous reports concluded, but the proportion of Fe3+ cations non-clustered is higher in smectites than in illites. This behavior supports the experimental behavior of the Fe effect on the Al-NMR signal, which is lower in illites than in smectites.

Computational study of the elastic behavior of the 2M1 muscovite-paragonite series

Abstract Elastic properties are an important issue in explaining the behavior of seisms and to ascertain the mineralogical composition of the Earth’s shells through which seismic waves pass. Computational methods can yield an additional, detailed, free-of-heterogeneity model knowledge of the mineral series of interest. Therefore, a computational study on the influence of the interlayer cation in the muscovite-paragonite (Ms-Pg) series on the crystal cell, internal geometry, and the elastic properties was made to shed light on the mineralogical, geophysical, and geochemical properties of the series. These properties have been calculated by means of Density Functional Theory (SIESTA2.0.2 code). The crystal structure and internal geometry agreed with the range of experimental values in the literature. In general, elastic stiffness constants (EC) agreed with the known experimental values. ECs of different interlayer cation configurations for the middle concentration sample showed very similar values, except for C33, The majority of ECs, with the exception of C33 and C66, decreased as a function of Na′ [Na/(Na+K)], many of which showed ideal crystalline solution behavior, and some showed mixing terms. The polycrystalline bulk modulus registered similar values for the end-members of the series and a minimum at Na′ = 0.5, although an estimate of the value at room temperature made the Pg stiffer than Ms; while the shear modulus showed a decreasing trend as a function of the Na′. Velocities of the sound waves lowered as a function of Na′. Local deformabilities were also studied, where the highest deformability was found for the interlayer space. The results are discussed in the framework of the mineralogical, geochemical, and geophysical knowledge of the series.

An ab initio comparative structural study of alkenylphosphonic acid derivatives

Abstract A comparative study of the electronic structure and conformational properties of alkenylphosphonic acid derivatives with different substituents has been carried out by means of ab initio quantum mechanical methods. The ab initio calculations have been performed using different basis sets. A strongly polarized partial triple bond for the phosphoryl group has been found. A very weak π conjugation has been detected in the C=C/P=O system. Intramolecular hydrogen bonds have been found in 2- cis -carboxyvinylphosphonic acid.

MOLECULAR STRUCTURE AND CONFORMATIONAL ANALYSIS OF CHIRAL ALCOHOLS. APPLICATION TO THE ENANTIOSELECTIVITY STUDY OF LIPASES

Abstract The molecular structures of the chiral compounds 1-phenylethanol, 2-hexanol and 1-phenylethanol acetate have been studied theoretically by ab initio methods. Conformational analysis and electronic structure studies have been carried out with these molecules at STO-3G ∗ and 6-31G ∗ basis sets. For the study of the interaction of lipases with substrates, a simplified model of the tetrahedral intermediate has been calculated at the 6-31G ∗ //4-31G ∗ level. Molecular mechanics simulations of the interaction of these compounds with the lipases of Candida rugosa, Pseudomonas cepacia and Rhizomucor miehei have been used to study the enantioselectivity of these lipases in the transesterification reaction of the chiral alcohols. The theoretical results have been compared with experimental data and good agreement was observed. It can be concluded that the enantioselectivity of these lipases is controlled by the formation of a tetrahedral intermediate, whereas Michaelis complex formation has a much lower significance.