RESUMEN

Copper squarate is a metal-organic framework with an oxo-carbonic anion organic linker and a doubly charged metal mode. Its structure features large channels that facilitate the adsorption of relatively small molecules. This study focuses on exploring the potential of adsorbing small pollutants, primarily greenhouse gases, with additional investigations conducted on larger pollutants. The objective is to comprehend the efficacy of this new material in single and multiple molecular adsorption processes using theoretical methods based on density functional theory. Furthermore, we find that the molecular adsorption energies range from 3.4 KJ∙mol-1 to 63.32 KJ∙mol-1 depending on the size and number of adsorbed molecules. An exception is noted with an unfavorable adsorption energy value of 47.94 KJ∙mol-1 for 4-nitrophenol. More importantly, we demonstrate that water exerts an inhibitory effect on the adsorption of these pollutants, distinguishing copper squarate as a rare MOF with hydrophilic properties. The Connolly surface was estimated to give a more accurate idea of the volume and surface accessibility of copper squarate. Finally, using Monte Carlo simulations, we present a study of adsorption isotherms for individual molecules and molecules mixed with water. Our results point out that copper squarate is an efficient adsorbent for small molecular pollutants and greenhouse gases.

RESUMEN

The density functional theory (DFT) is applied to theoretically study the capture and storage of three different nitro polycyclic aromatic hydrocarbons, 4-nitrophenol, 2-nitrophenol, and 9-nitroanthracene by activated carbon, with and without the presence of water. These species are pollutants derived from vehicle and industry emissions. The modeling of adsorption is carried out at the molecular level using a high-level density functional theory with the B3LYP-GD(BJ)/6-31+G(d,p) level of theory. The adsorption energies of polluting gases considered isolated and in a humid environment are compared to better understand the role of water. The calculations reveal different possible pathways involving the formation of chemical bonds between adsorbent and adsorbate on the formation of intermolecular van der Waals interactions. The negative adsorption energy on AC for the three species is obtained when they are treated individually and in mixture with H2O. The basis-set superposition error, estimated using the counterpoise correction, varies the adsorption energies by 2-13%. Dispersion effects were also taken into account. The adsorption energy ranges from -10 to -414 kJ/mol suggesting a diversity of pathways. The resulting analysis suggests three preferred pathways for capture. The main pathway is physical interaction due to π-π stacking. Other means are capture due to the formation of hydrogen bonds resulting from water adsorbed on the surface and the simultaneous adsorption of pollutant and water where water can act as a link that promotes adsorption. The thermodynamic properties give a clue to the most eco-friendly approaches for molecular adsorption.

RESUMEN

Urea is a molecule of great interest in chemistry and biology. In particular, it is considered a key building block in prebiotic chemistry on Earth. The hypothesis of its possible exogenous origin has been reinforced after the recent detection of this molecule in the interstellar medium, where it is believed to form in the ice mantles of dust grains. In this work the infrared spectra of urea ices and urea:H2O ice mixtures have been studied both experimentally and theoretically. Urea ices were generated by vapour deposition at temperatures between 10 K and 270 K. It was found that an amorphous phase is formed at temperatures below 200 K. A theoretical modelling of crystalline urea and of a tentative amorphous urea solid phase, as well as of amorphous urea:H2O ice mixtures, has been performed. The corresponding infrared spectra were simulated with density functional theory. The main spectral features observed in the various solid samples are interpreted with the help of the theoretical results. Infrared band strengths are also provided for amorphous and crystalline urea. The infrared spectroscopic information given in this work is expected to be useful for the detection and quantification of urea in astrophysical ices.

RESUMEN

The determination of the full crystal structure of the uranyl sulfate mineral uranopilite, (UO2)6(SO4)O2(OH)6·14H2O, including the positions of the hydrogen atoms within the corresponding unit cell, has not been feasible to date due to the poor quality of its X-ray diffraction pattern. In this paper, the complete crystal structure of uranopilite is established for the first time by means of first principles solid-state calculations based in density functional theory employing a large plane wave basis set and pseudopotential functions. The computed unit-cell parameters and structural data for the non-hydrogen atoms are in excellent agreement with the available experimental data. The computed X-ray diffraction pattern is also in satisfactory agreement with the experimental pattern. The infrared spectrum of uranopilite is collected from a natural crystal specimen originating in Jáchymov (Czech Republic) and computed employing density functional perturbation theory. The theoretical and experimental vibrational spectra are highly consistent. Therefore, a full assignment of the bands in the experimental infrared spectrum is performed using a normal mode analysis of the first principles vibrational results. One overtone and six combination bands are recognized in the infrared spectrum. The elasticity tensor and phonon spectra of uranopilite are computed from the optimized crystal structure and used to analyze its mechanical stability, to obtain a rich set of elastic properties and to derive its fundamental thermodynamic properties as a function of temperature. Uranopilite is shown to have a large mechanical anisotropy and to exhibit the negative Poisson's ratio and negative linear compressibility phenomena. The calculated specific heat and entropy at 298.15 K are 179.6 and 209.0 J K-1 mol-1, respectively. The computed fundamental thermodynamic functions of uranopilite are employed to obtain its thermodynamic functions of formation in terms of the elements and the thermodynamic properties of a set of chemical reactions relating uranopilite with a representative group of secondary phases of spent nuclear fuel. From the reaction thermodynamic data, the relative stability of uranopilite with respect to these secondary phases is evaluated as a function of temperature and under different hydrogen peroxide concentrations. From the results, it follows that uranopilite has a very large thermodynamic stability in the presence of hydrogen peroxide. The high stability of uranopilite under this condition justify its early crystallization in the paragenetic sequence of secondary phases occurring when uranium dioxide is exposed to sulfur-rich solutions.

RESUMEN

The mechanical properties of the uranyl squarate monohydrate material, [Formula: see text], were studied using theoretical solid-state methods based in density functional theory employing plane waves and pseudopotentials. Very demanding calculation parameters were utilized in order to obtain a realistic description of the mechanical behavior of this material. Since the determination of the positions of the hydrogen atoms in the unit cell of uranyl squarate monohydrate was not possible from x-ray diffraction data by structure refinement, they were fully optimized theoretically. The computed lattice parameters, bond distances, angles, and x-ray powder diffraction patterns of this material were in very good agreement with the experimental data. This material was found to be mechanically and dynamically stable since the corresponding stability conditions were satisfied. The values of the bulk modulus and its pressure derivatives, shear and Young moduli, Poisson ratio, ductility, hardness, and mechanical anisotropy indices of this material were reported. Furthermore, this study showed that this material exhibits the important negative Poisson ratio (NPR) and negative linear compressibility (NLC) phenomena. Uranyl squarate monohydrate is a very anisotropic brittle material characterized by a bulk modulus of ~33 GPa, which shows a minimum value of the NPR of the order of -0.5. Besides, this material displays NLC values for a limited range of positive pressures, from 0.025 GPa to 0.094 GPa, applied along the direction of minimum negative Poisson ratio. The analysis of the crystal structure as a function of pressure demonstrates that the mechanism of NLC of this material is associated to the change in shape of the uranyl pentagonal bipyramids and unrelated to the wine-rack structural mechanism commonly used to rationalize this phenomenon.

RESUMEN

The full crystal structure of the copper-uranyl tetrahydroxide mineral (vandenbrandeite), including the positions of the hydrogen atoms, is established by the first time from X-ray diffraction data taken from a natural crystal sample from the Musonoi Mine, Katanga Province, Democratic Republic of Congo. The structure is verified using first-principles solid-state methods. From the optimized structure, the mechanical and dynamical stability of vandenbrandeite is studied and a rich set of mechanical properties are determined. The Raman spectrum is recorded from the natural sample and determined theoretically. Since both spectra have a high-degree of consistence, all spectral bands are rigorously assigned using a theoretical normal-coordinate analysis. Two bands in the Raman spectra, located at 2327 and 1604 cm-1, are recognized as overtones and a band at 1554 cm-1 is identified as a combination band. The fundamental thermodynamic functions of vandenbrandeite are computed as a function of temperature using phonon calculations. These properties, unknown so far, are key-parameters for the performance-assessment of geological repositories for storage of radioactive nuclear waste and for understanding the paragenetic sequence of minerals arising from the corrosion of uranium deposits. The thermodynamic functions are used here to determine the thermodynamic properties of formation of vandenbrandeite in terms of the elements and the Gibbs free-energies and reaction constants for a series of reactions involving vandenbrandeite and a representative subset of the most important secondary phases of spent nuclear fuel. Finally, from the thermodynamic data of these reactions, the relative stability of vandenbrandeite with respect to these phases as a function of temperature and in the presence of hydrogen peroxide is evaluated. Vandenbrandeite is shown to be highly stable under the simultaneous presence of water and hydrogen peroxide.

RESUMEN

The crystal structure, hydrogen bonding, mechanical properties and Raman spectrum of the lead uranyl silicate monohydrate mineral kasolite, Pb(UO2)(SiO4)·H2O, are investigated by means of first-principles solid-state methods based on density functional theory using plane waves and pseudopotentials. The computed unit cell parameters, bond lengths and angles and X-ray powder pattern of kasolite are found to be in very good agreement with their experimental counterparts. The calculated hydrogen atom positions and associated hydrogen bond structure in the unit cell of kasolite confirmed the hydrogen bond scheme previously determined from X-ray diffraction data. The kasolite crystal structure is formed from uranyl silicate layers having the uranophane sheet anion-topology. The lead ions and water molecules are located in the interlayer space. Water molecules belong to the coordination structure of lead interlayer ions and reinforce the structure by hydrogen bonding between the uranyl silicate sheets. The hydrogen bonding in kasolite is strong and dual, that is, the water molecules are distributed in pairs, held together by two symmetrically related hydrogen bonds, one being directed from the first water molecule to the second one and the other from the second water molecule to the first one. As a result of the full structure determination of kasolite, the determination of its mechanical properties and Raman spectrum becomes possible using theoretical methods. The mechanical properties and mechanical stability of the structure of kasolite are studied using the finite deformation technique. The bulk modulus and its pressure derivatives, the Young and shear moduli, the Poisson ratio and the ductility, hardness and anisotropy indices are reported. Kasolite is a hard and brittle mineral possessing a large bulk modulus of the order of B ∼ 71 GPa. The structure is mechanically stable and very isotropic. The large mechanical isotropy of the structure is unexpected since layered structures are commonly very anisotropic and results from the strong dual hydrogen bonding among the uranyl silicate sheets. The experimental Raman spectrum of kasolite is recorded from a natural mineral sample from the Jánská vein, Príbram base metal ore district, Czech Republic, and determined by using density functional perturbation theory. The agreement is excellent and, therefore, the theoretical calculations are employed to assign the experimental spectrum. Besides, the theoretical results are used to guide the resolution into single components of the bands from the experimental spectrum. A large number of kasolite Raman bands are reassigned. Three bands of the experimental spectrum located at the wavenumbers 1015, 977 and 813 cm-1, are identified as combination bands.

RESUMEN

The structure and Raman spectrum of schoepite mineral, [(UO2)8O2(OH)12]·12H2O, was studied by means of theoretical calculations. The computations were carried out by using density functional theory with plane waves and pseudopotentials. A norm-conserving pseudopotential specific for the U atom developed in a previous work was employed. Because it was not possible to locate H atoms directly from X-ray diffraction (XRD) data by structure refinement in previous experimental studies, all of the positions of the H atoms in the full unit cell were determined theoretically. The structural results, including the lattice parameters, bond lengths, bond angles, and powder XRD pattern, were found to be in good agreement with their experimental counterparts. However, the calculations performed using the unit cell designed by Ostanin and Zeller in 2007, involving half of the atoms of the full unit cell, led to significant errors in the computed powder XRD pattern. Furthermore, Ostanin and Zeller's unit cell contains hydronium ions, H3O+, which are incompatible with the experimental information. Therefore, while the use of this schoepite model may be a very useful approximation requiring a much smaller amount of computational effort, the full unit cell should be used to study this mineral accurately. The Raman spectrum was also computed by means of density functional perturbation theory and compared with the experimental spectrum. The results were also in agreement with the experimental data. A normal-mode analysis of the theoretical spectra was performed to assign the main bands of the Raman spectrum. This assignment significantly improved the current empirical assignment of the bands of the Raman spectrum of schoepite mineral. In addition, the equation of state and elastic properties of this mineral were determined. The crystal structure of schoepite was found to be stable mechanically and dynamically. Schoepite can be described as a brittle material exhibiting small anisotropy and large compressibility in the direction perpendicular to the layers, which characterize its structure. The calculated bulk modulus, B, was ∼35 GPa.

RESUMEN

The structure, thermodynamic and mechanical properties of becquerelite mineral, Ca(UO2)6O4(OH)6·8H2O, were studied by means of theoretical solid-state calculations based on density functional theory using plane waves and pseudopotentials. The positions of the hydrogen atoms in the unit cell of becquerelite mineral were optimized theoretically since it was not possible to determine them from X-ray diffraction data by structure refinement. The structural results, including the lattice parameters, bond lengths and X-ray powder pattern, were found to be in excellent agreement with their experimental counterparts. The fundamental thermodynamic properties of becquerelite mineral, including specific heat, entropy, enthalpy and Gibbs free energy, were then computed by performing phonon calculations at the computed optimized structure. Since the experimental values of these properties are unknown, their values were predicted. The values obtained for the isobaric specific heat and entropy of becquerelite at the temperature of 298.15 K were 148.4 and 172.3 J K-1 mol-1, respectively. The computed thermodynamic properties were combined with those of the corresponding elements in order to obtain the enthalpy and Gibbs free energy of formation as a function of temperature. The availability of these thermodynamic properties of formation allowed to determine the enthalpies and free energies and associated reaction constants of a series of reactions involving becquerelite and other uranyl containing materials. Futhermore, knowledge of these properties permitted the study of the thermodynamic stability of becquerelite with respect to a rich set of secondary phases of spent nuclear fuel, including dehydrated schoepite, schoepite, metaschoepite, studtite, metastudtite, rutherfordine and soddyite under different conditions of temperature. Becquerelite is shown to be highly stable in the presence of hydrogen peroxide. It is the second most stable phase under intermediate hydrogen peroxide concentrations (after schoepite), and the fourth most stable phase under high hydrogen peroxide concentrations (after studtite, schoepite and metaschoepite). Finally, the equation of state and elastic properties of this mineral, unknown to date, were determined. The crystal structure of becquerelite was found to be stable mechanically and dynamically. Becquerelite can be described as a brittle material exhibiting large anisotropy and large compressibility in the direction perpendicular to the sheets characterizing the structure of this layered uranyl containing material. The dependence of the elastic properties of becquerelite with respect to the strain orientation is shown to be analogous to that of schoepite mineral. The calculated bulk modulus is also very similar to that of schoepite, B ∼ 31 GPa.

RESUMEN

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.

RESUMEN

A theoretical study of the structure and mid infrared (IR) spectra of interstellar hydrocarbon dust analogs is presented, based on DFT calculations of amorphous solids. The basic molecular structures for these solids are taken from two competing literature models. The first model considers small aromatic units linked by aliphatic chains. The second one assumes a polyaromatic core with hydrogen and methyl substituents at the edges. The calculated spectra are in reasonably good agreement with those of aliphatic-rich and graphitic-rich samples of hydrogenated amorphous carbon (HAC) generated in our laboratory. The theoretical analysis allows the assignment of the main vibrations in the HAC spectra and shows that there is a large degree of mode mixing. The calculated spectra show a marked dependence on the density of the model solids, which evinces the strong influence of the environment on the strengths of the vibrational modes. The present results indicate that the current procedure of estimating the hydrogen and graphitic content of HAC samples through the decomposition of IR features into vibrational modes of individual functional groups is problematic owing to the mentioned mode mixing and to the difficulty of assigning reliable and unique band strengths to the various molecular vibrations. Current band strengths from the literature might overestimate polyaromatic structures. Comparison with astronomical observations suggests that the average structure of carbonaceous dust in the diffuse interstellar medium lies probably in between those of the two models considered, though closer to the more aliphatic structure.

RESUMEN

A theoretical model of hydrogenated amorphous carbon (HAC) is developed and applied to study the interaction of glycine with HAC surfaces at astronomical temperatures. Two models with different H content are tried for the HAC surface. The theory is applied at the Density Functional Theory (DFT) level, including a semiempirical dispersion correlation potential, d-DFT or Grimme DFT-D2. The level of theory is tested on glycine adsorption on a Si(001) surface. Crystalline glycine is also studied in its two stable phases, α and ß, and the metastable γ phase. For the adsorption on Si or HAC surfaces, molecular glycine is introduced in the neutral and zwitterionic forms, and the most stable configurations are searched. All theoretical predictions are checked against experimental observations. HAC films are prepared by plasma enhanced vapor deposition at room temperature. Glycine is deposited at 20 K into a high vacuum, cold temperature chamber, to simulate astronomical conditions. Adsorption takes place through the acidic group COO(-) and when several glycine molecules are present, they form H-bond chains among them. Comparison between experiments and predictions suggests that a possible way to improve the theoretical model would require the introduction of aliphatic chains or a polycyclic aromatic core. The lack of previous models to study the interaction of amino-acids with HAC surfaces provides a motivation for this work.

Asunto(s)

Carbono/química , Glicina/química , Modelos Teóricos , Adsorción , Enlace de Hidrógeno , Hidrogenación , Silicio/química , Propiedades de Superficie , Temperatura

RESUMEN

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.

RESUMEN

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 Marcus's 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.