Reactions of One-Electron-Oxidized Methionine with Oxygen: An ab initio study

A one-electron oxidation of a methionine residue is thought to be a key step in the neurotoxicity of the beta amyloid peptide of Alzheimer's disease. The chemistry of the radical cation of N-formylmethioninamide (11+) and two model systems, dimethyl sulfide (1+) and ethyl methyl sulfide (6+), in the presence of oxygen have been studied by B3LYP/6-31G(d) and CBS-RAD calculations. The stable form of 11+ has a three-electron bond between the sulfur radical cation and the carbonyl oxygen atom of the i - 1 residue. The radical cation may lose a proton from the methyl or methylene groups flanking the oxidized sulfur. Both 11+ and the resultant C-centered radicals may add oxygen to form peroxy radicals. The calculations indicate that unlike C-centered radicals the sulfur radical cation does not form a covalent bond to oxygen but rather forms a loose ion-induced dipole complex with an S-O separation of about 2.7 Å, and is bound by about 13 kJ mol-1 (on the basis of 1+ + O2). Direct intramolecular abstraction of an H atom from the C site is unlikely. It is endothermic by more than 20 kJ mol-1 and involves a high barrier (G = 79 kJ mol-1). The -to-S C-centered radicals will add oxygen to form peroxy radicals. The OH BDEs of the parent hydroperoxides are in the range of 352-355 kJ mol-1, similar to SH BDEs (360 kJ mol-1) and C-H BDEs (345-350 kJ mol-1). Thus, the peroxy radicals are oxidizing species comparable in strength to thiyl radicals and peptide backbone C-centered radicals. Each peroxy radical can abstract a hydrogen atom from the backbone C site of the Met residue to yield the corresponding C-centered radical/hydroperoxide in a weakly exothermic process with modest barriers in the range of 64-92 kJ mol-1.

Polarization Relaxation in an Ionic Liquid Confined between Electrified Walls

The response of a room temperature molten salt to an external electric field when it is confined to a nanoslit is studied by molecular dynamics simulations. The fluid is confined between two parallel and oppositely charged walls, emulating two electrified solid-liquid interfaces. Attention is focused on structural, electrostatic, and dynamical properties, which are compared with those of the nonpolarized fluid. It is found that the relaxation of the electrostatic potential, after switching the electric field off, occurs in two stages. A first, subpicosecond process accounts for 80% of the decay and is followed by a second subdiffusive process with a time constant of 8 ps. Diffusion is not involved in the relaxation, which is mostly driven by small anion translations. The relaxation of the polarization in the confined system is discussed in terms of the spectrum of charge density fluctuations in the bulk.

Neutral and Charged 1-Butyl-3-methylimidazolium Triflate Clusters: Equilibrium Concentration in the Vapor Phase and Thermal Properties of Nanometric Droplets

Ground state energy, structure, and harmonic vibrational modes of 1-butyl-3-methylimidazolium triflate ([bmim][Tf]) clusters have been computed using an all-atom empirical potential model. Neutral and charged species have been considered up to a size (30 [bmim][Tf] pairs) well into the nanometric range. Free energy computations and thermodynamic modeling have been used to predict the equilibrium composition of the vapor phase as a function of temperature and density. The results point to a nonnegligible concentration of very small charged species at pressures (P ~ 0.01 Pa) and temperatures (T 600 K) at the boundary of the stability range of [bmim][Tf]. Thermal properties of nanometric neutral droplets have been investigated in the 0 T 700 K range. A near-continuous transition between a liquidlike phase at high T and a solidlike phase at low T takes place at T ~ 190 K in close correspondence with the bulk glass point Tg ~ 200 K. Solidification is accompanied by a transition in the dielectric properties of the droplet, giving rise to a small permanent dipole embedded into the solid cluster. The simulation results highlight the molecular precursors of several macroscopic properties and phenomena and point to the close competition of Coulomb and dispersion forces as their common origin.

Structure and dynamics of a confined ionic liquid. topics of relevance to dye-sensitized solar cells

The behavior of a model ionic liquid (IL) confined between two flat parallel walls was studied at various interwall distances using computer simulations. The results focus both on structural and dynamical properties. Mass and charge density along the confinement axis reveal a structure of layers parallel to the walls that leads to an oscillatory profile in the electrostatic potential. Orientational correlation functions indicate that cations at the interface orient tilted with respect to the surface and that any other orientational order is lost thereafter. The diffusion coefficients of the ions exhibit a maximum as a function of the confinement distance, a behavior that results from a combination of the structure of the liquid as a whole and a faster molecular motion in the vicinity of the walls. We discuss the relevance of the present results and elaborate on topics that need further attention regarding the effects of ILs in the functioning of IL-based dye-sensitized solar cells.

Simulation of interfaces between room temperature ionic liquids and other liquids

The structure and properties of the interfaces between the room temperature ionic liquid dimethylimidazolium chloride ([dmim]Cl) and different Lennard-Jones fluids and between ionic liquid and water have been studied by molecular dynamics simulations, and compared to the ionic liquid-vapour interface. Two contrasting types of interface were investigated, thermodynamically stable interfaces between ionic liquid and vapour and between ionic liquid and Lennard-Jones fluids, and diffusing interfaces between miscible phases of different compositions involving water. The density profiles of different species through the interface are presented. The cations and water molecules near the former type of interface are aligned relative to the surface, but no orientational preference was found near or in the broad diffusing interface. The ionic liquid has a negative electrostatic potential relative to vapour or Lennard-Jones fluid, but is more positive than pure water. This contrast is explained in terms of the relative importance of orientation and concentration differences in the two types of interface.

Conformations, vibrational frequencies and Raman intensities of short-chain fatty acid methyl esters using DFT with 6-31G(d) and Sadlej pVTZ basis sets

Density functional calculations, using B3LPY/6-31G(d) methods, have been used to investigate the conformations and vibrational (Raman) spectra of three short-chain fatty acid methyl esters (FAMEs) with the formula CnH2nO2 (n = 3-5). In all three FAMEs, the lowest energy conformer has a simple 'all-trans' structure but there are other conformers, with different torsions about the backbone, which lie reasonably close in energy to the global minimum. One result of this is that the solid samples we studied do not appear to consist entirely of the lowest energy conformer. Indeed, to account for the 'extra' bands that were observed in the Raman data but were not predicted for the all-trans conformer, it was necessary to add-in contributions from other conformers before a complete set of vibrational assignments could be made. Provided this was done, the agreement between experimental Raman frequencies and 6-31G(d) values (after scaling) was excellent, RSD = 12.6 cm(-1). However, the agreement between predicted and observed intensities was much less satisfactory. To confirm the validity of the approach followed by the 6-3 1 G(d) basis set, we used a larger basis set, Sadlej pVTZ, and found that these calculations gave accurate Raman intensities and simulated spectra (summed from two different conformers) that were in quantitative agreement with experiment. In addition, the unscaled Sadlej pVTZ, and the scaled 6-3 1 G(d) calculations gave the same vibrational mode assignments for all bands in the experimental data. This work provides the foundation for calculations on longer-chain FAMEs (which are closer to those found as triglycerides in edible fats and oils) because it shows that scaled 6-3 1 G(d) calculations give equally accurate frequency predictions, and the same vibrational mode assignments, as the much more CPU-expensive Sadlej pVTZ basis set calculations.

Understanding the dehydrogenation mechanism of tetrahydrocarbazole over palladium using a combined experimental and density functional theory approach

The mechanism of the dehydrogenation of tetrahydrocarbazole to carbazole over palladium has been examined for the first time. By use of a combination of deuterium exchange experiments and density functional theory calculations, a detailed reaction profile for the aromatization of tetrahydrocarbazole has been identified and validated by experiment. As with many dehydrogenation reactions, the initial hydrogen abstraction is found to have the highest reaction barrier. Tetrahydrocarbazole has four hydrogens which can, in principle, be cleaved initially; however, the theory and experiment show that the reaction is dominated by the cleavage of the carbon hydrogens at the carbon atoms in positions 1 and 4. The two pathways originating from these two C-H bond cleavage processes are found to have similar reaction energy profiles and both contribute to the overall reaction.

Resonance Raman and lifetime studies on regioselectively deuteriated ruthenium (II) polypyridyl complexes

Two series of ruthenium(II) polypyridyl complexes [Ru(bipy)2(phpytr)]+ and [Ru(bipy)2(phpztr)]+ (where Hphpytr = 2-(5-phenyl-1H-[1,2,4]triazol-3-yl)-pyridine and Hphpztr = 2-(5-phenyl-1H-[1,2,4]triazol-3-yl)-pyrazine) are examined by electrochemistry, UV/Vis, emission, resonance Raman, transient resonance Raman and transient absorption spectroscopy, in order to obtain a more comprehensive understanding of their excited state electronic properties. The interpretation of the results obtained is facilitated by the availability of several isotopologues of each of the complexes examined. For the pyridine-1,2,4-triazolato based complex the lowest emissive excited state is exclusively bipy based, however, for the pyrazine based complexes excited state localisation on particular ligands shows considerable solvent and pH dependency.

Raman and ab initio studies of simple and binary 1-Alkyl-3-methylimidazolium ionic liquids

Raman spectra of the ionic liquids, 1-butyl-3-methylimidazolium hexafluorophosphate ([C(4)mim][PF(6)]), 1-hexyl-3-methylimidazolium chloride ([C(6)mim]Cl), and 1-hexyl-3-methylimidazolium hexafluorophosphate ([C(6)mim][PF(6)]), and binary mixtures thereof, have been assigned using ab initio MP2 calculations. The previously reported anti and gauche forms of the [C(4)mim](+) cation have been observed, and this study reveals this to be a general feature of the long-chain I-alkyl derivatives. Analysis of mixtures Of [C(6)mim]Cl and [C(6)mim][PF(6)] has provided information on the nature of the hydrogen bonding between the imidazolium headgroup and the anions, and the invariance of the essentially 50:50 mixture of the predominant conformers informs on the nature of glass formation in these systems.

On the origin of the forward peak and backward oscillations in the F + H2(v = 0) to HF(v' = 2) + H reaction

We present a semiclassical complex angular momentum (CAM) analysis of the forward scattering peak which occurs at a translational collision energy around 32 meV in the quantum mechanical calculations for the F + H2(v = 0, j = 0) ? HF(v' = 2, j' = 0) + H reaction on the Stark–Werner potential energy surface. The semiclassical CAM theory is modified to cover the forward and backward scattering angles. The peak is shown to result from constructive/destructive interference of the two Regge states associated with two resonances, one in the transition state region and the other in the exit channel van der Waals well. In addition, we demonstrate that the oscillations in the energy dependence of the backward differential cross section are caused by the interference between the direct backward scattering and the decay of the two resonance complexes returning to the backward direction after one full rotation.

Viscosity of binary mixtures of cycloalkane with cycloalkane, alkane and aromatic hydrocarbon at 303.15 K

The viscosity ? for eighteen binary mixtures cyclopentane + cyclohexane and + cyclooctane; cyclohexane + cycloheptane, + cyclooctane, + methylcyclohexane, + n-hexane, + n-heptane, + n-octane, + i-octane, + benzene, + toluene, + ethylbenzene, + p-xylene, and + propylbenzene; methylcyclohexane + n-hexane, + i-octane, and + benzene; and cyclooctane + benzene have been reported at 303.15 K over the entire range of composition. The viscosity deviations ?? and excess Gibbs energy of activation ?G*E of viscous flow based on Eyring's theory have been calculated. The effects of molecular sizes and shapes of the component molecules and of interaction energy in the mixture have been discussed. The viscosity data have been correlated with the equations of Grunberg and Nissan, Hind, McLaughlin and Ubbelohde, Tamura and Kurata, Katti and Chaudhri, McAllister, Heric and Brewer, and of Auslaender.

Speeds of sound and isentropic compressibilities of binary mixtures containing trialkylamines with alkanes and mono-alkylamines at 303.15 and 313.15 K

Isentropic compressibilities ?S, and excess isentropic compressibilities ?SE have been determined from measurements of speeds of sound u and densities ? of 14 binary mixtures of triethylamine (TEA) and tri-n-butylamine (TBA) with n-hexane, n-octane, iso-octane, n-propylamine, n-butylamine, n-hexylamine and n-octylamine. The relative magnitude and sign of ?SE have been interpreted in terms of molecular interactions and interstitial accommodation. The values of ?SE for TEA + alkane are positive while for TBA + alkane are negative. The values of ?SE for TEA + primary amine become progressively less positive and eventually to negative with the increase in chain length of alkylamine. In case of TBA + primary amine, the values of ?SE increase from n-propylamine to n-butylamine, and then decrease with chain length of primary amine. The experimental speeds of sound u have been analyzed in terms of collision factor theory, free length theory and Prigogine–Flory–Patterson statistical theory of solutions.