Molecular structure and spectroscopic properties of polyaromatic heterocycles by first principle calculations: spectroscopic shifts with the adsorption of thiophene on phyllosilicate surface

The molecular and electronic structure and spectroscopic properties of thiophene, benzothiophene, and dibenzothiophene molecules have been studied theoretically, using different levels of quantum-mechanical calculations based on Hartree–Fock and density functional theory (DFT) approximations. In all calculation levels used, the molecular structures, dipole moments, thermodynamic properties, and vibration normal modes agree well with the available experimental data and predict the non-available values. The calculated frequencies agree with experimental values within scale factors in the range of 0.94–1.0 for thiophene. Our calculations have refined the mode assignments previously reported. The adsorption of thiophene on a pyrophyllite surface along the 001 plane was also investigated by means of a quantum-mechanical method based on the DFT approximation in a periodical crystal lattice model. The adsorbed thiophene adopts a parallel orientation with respect to the phyllosilicate surface. The shifts observed experimentally in the IR bands of thiophene upon adsorption on pyrophyllite are well reproduced in the thiophene–phyllosilicate complex, finding explanations of this phenomenon and new effects with our calculations

Quantum chemistry and computational kinetics of the reaction between OH radicals and formaldehyde adsorbed on small silica aerosol models

11 pages, 4 tables, 16 figures.Heterogeneous reactions of atmospheric volatile organic compounds (VOCs) on aerosol particles may play an important role in atmospheric chemistry. Clay particles are present in mineral dust in atmospheric aerosols, and radical reactions are thought to be heterogeneously catalyzed on them. However, the kinetics and mechanisms of adsorption and reaction of atmospheric VOCs on aerosol surfaces are not well understood. In this work, quantum chemical methods are used to study the reaction of OH radicals with formaldehyde adsorbed on small (SiO4)n cluster models, with n = 1 to 6. We show that surface adsorbed formaldehyde can react in the presence of gas-phase OH radicals to yield surface-bound formyl radicals and water. Significant exothermic adsorption energies are found, supporting the notion that silicate surfaces are good quenchers of VOCs. With the models employed, the reaction appears to be less favored on the silicate surfaces than in the gas phase. The effect of the model surface on the reaction mechanism is analyzed.Authors are thankful to the Mexican agency CONACYT through Grant SEP-2004-C01-46167 and to PIFI 3.3 for the acquisition of computer clusters on which calculations were performed. This work was also supported by an international cooperation project CSIC-CONACYT (ref 2004MX0017) and the Spanish MCYT and European FEDER Grants BTE2002-03838, and CTQ2004-04648.Peer reviewe

ROS Initiated Oxidation of Dopamine under Oxidative Stress Conditions in Aqueous and Lipidic Environments

Dopamine is known to be an efficient antioxidant and to protect neurocytes from oxidative stress by scavenging free radicals. In this work, we have carried out a systematic quantum chemistry and computational kinetics study on the reactivity of dopamine toward hydroxyl (•OH) and hydroperoxyl (•OOH) free radicals in aqueous and lipidic simulated biological environments, within the density functional theory framework. Rate constants and branching ratios for the different paths contributing to the overall reaction, at 298 K, are reported. For the reactivity of dopamine toward hydroxyl radicals, in water at physiological pH, the main mechanism of the reaction is proposed to be the sequential electron proton transfer (SEPT), whereas in the lipidic environment, hydrogen atom transfer (HAT) and radical adduct formation (RAF) pathways contribute almost equally to the total reaction rate. In both environments, dopamine reacts with hydroxyl radicals at a rate that is diffusion-controlled. Reaction with the hydroperoxyl radical is much slower and occurs only by abstraction of any of the phenolic hydrogens. The overall rate coefficients are predicted to be 2.23 × 10⁵ and 8.16 × 10⁵ M^–1 s^–1, in aqueous and lipidic environment, respectively, which makes dopamine a very good •OOH, and presumably •OOR, radical scavenger

Interaction Energies and Spectroscopic Effects in the Adsorption of Formic Acid on Mineral Aerosol Surface Models

Heterogeneous reactions of atmospheric volatile organic compounds (VOCs) on aerosol particles may play an important role in atmospheric chemistry. Silicate particles are present in airborne mineral dust in aerosols, and the atmospheric chemistry in general can be modified by their presence. In this work, the adsorption of a single formic acid molecule on different silicate surface models has been studied using quantum-mechanical methods. Both molecular clusters and a periodic crystal model of the (001) pyrophyllite surface have been employed, and all possible adsorption geometries have been considered. We find that silanol groups are always the most reactive formic acid adsorption sites. In the case of a periodic system, silanol groups at the crystal edges are favored. However, OH groups on the phyllosilicate octahedral sheet are also reactive sites through the tetrahedral cavities. The effect of formic acid adsorption on the spectroscopic properties of the whole system is also analyzed. Significant frequency shifts are detected in the vibration modes of both adsorbate and surface models. These results can be a useful tool for experimental adsorption investigations using vibration spectroscopy