Ab initio molecular dynamics simulation of a room temperature ionic liquid

Ab initio molecular dynamics simulations have been performed for the first time on the room-temperature organic ionic liquid dimethyl imidazolium chloride [DMIM][Cl] using density functional theory. The aim is to compare the local liquid structure with both that obtained from two different classical force fields and from neutron scattering experiments. The local structure around the cation shows significant differences compared to both the classical calculations and the neutron results. In particular, and unlike in the gas-phase ion pair, chloride ions tend to be located near a ring C-H proton in a position suggesting hydrogen bonding. The results are used to suggest ways in which the classical potentials may be improved.     

Atomistic molecular dynamics simulations of chemical force microscopy

Chemical force microscopy and related force measurement techniques have emerged as powerful tools for studying fundamental interactions central to understanding adhesion and tribology at the molecular scale. However, detailed interpretation of these interactions requires knowledge of chemical and physical processes occurring in the region of the tip-sample junction that experiments cannot provide, such as atomic-scale motions and distribution of forces. In an effort to address some of these open issues, atomistic molecular dynamics simulations were performed modeling a chemical force microscope stylus covered with a planar C12 alkylthiolate self-assembled monolayer (SAM) interacting with a solid wall. A complete loading-unloading sequence was simulated under conditions of near-constant equilibrium, approximating the case of infinitely slow tip motion. In the absence of the solid wall, the stylus film existed in a fluid state with structural and dynamic properties similar to those of the analogous planar SAM at an elevated temperature. When the wall was brought into contact with the stylus and pressed against it, a series of reversible changes occurred culminating with solidification of the SAM film at the largest compressive force. During loading, the chemical composition of the contact changed, as much of the film's interior was exposed to the wall. At all tip heights, the distribution of forces within the contact zone was uneven and subject to large local fluctuations. Analysis using the Johnson-Kendall-Roberts, Derjaguin-Muller-Toporov, and Hertz contacts mechanics models revealed significant deviations from the simulation results, with the JKR model providing best overall agreement. Some of the discrepancies found would be overlooked in an actual experiment, where, unlike the simulations, contact area is not separately known, possibly producing a misleading or incorrect interpretation of experimental results. These shortcomings may be improved upon by using a model that correctly accounts for the finite thickness of the compliant components and nonlinear elastic effects.     

Macroscopic and microscopic properties of solutions of aromatic compounds in an ionic liquid

Molecular dynamics simulations of binary mixtures of benzene, 1,3,5-trifluorobenzene and hexafluorobenzene with dimethylimidazolium hexafluorophosphate were carried out to examine their macroscopic and microscopic properties. The energies and volumes of mixing of these mixtures correlate well with observed microscopic properties including coordination number about the aromatic compound. The local ordering of the ions about an aromatic molecule was found to depend on the quadrupole moment of the aromatic species and to remain qualitatively the same on varying the mole fraction of the aromatic species. Interaction energies showed the most significant interactions to be between the aromatic molecule and the ions located about its equator. These findings have implications for the practical use of ionic liquids as solvents for chemical processes.     

A density matrix formulation of the theory of magnetic resonance spectra in slowly reorienting systems

When a spin system is coupled to a molecule or part of a molecule which is reorienting at a rate comparable to the width of the powder spectrum, the line shape can be calculated from a density matrix which is a function both of spin operators and of the Euler angles describing the molecular orientation. The problem of calculating such line shapes is eased by using the super-operator formalism and choosing symmetry adapted basis operators in the Liouville space of spins and orientations. Diffusion and strong collision models for molecular reorientation are discussed.     

Os(VIII)-catalysed oxidation of sulfides by sodium salt of N-chlorobenzenesulfonamide

Catalytic activity of Os(VIII) in the oxidation of some twenty organic sulfides with sodium salt of N-chlorobenzenesulfonamide (CAB) has been investigated in alkaline (pH8.7) t-butanol–water (1:1 v/v) medium. Significant retarding influence of [OH⁻] on the reactivity is exhibited. The catalysed reaction is strongly accelerated in the presence of Hg(II). Imperfections are observed in the linear Hammett relationship in the case of –NO₂ substituents.     

The pathway to reorientation in ammonium fluoride

Two alternative transition states for ammonium ion rotation in crystalline NH₄F have been characterised using ab initio calculations. In one all the cations rotate in phase, while in the other the rotating ions are isolated from each other by non-rotated ions. These two transition states are characterised by the cation displacement and changes in the bond lengths and bond angles within the ammonium ion. The pathway for passing over the barrier was investigated by low temperature molecular dynamics runs from each transition state. In both cases the order of events in passing from the ground state to the transition state is first cation displacement towards a neighbouring fluoride ion, secondly, lengthening of the NH bond pointing to this ion, and thirdly, rotation about this bond.     

Raman spectroscopic investigation on the microenvironment of the liver tissues of Zebrafish (Danio rerio) due to titanium dioxide exposure

Nano titanium dioxide (nTiO₂), generally considered to be toxicologically inert, is manufactured in large quantities and extensively applied in consumer products. The small size and large surface area endow them with an active group or intrinsic toxicity. Advances in instrumentation are making Raman spectroscopy the tool of choice for an increasing number of (bio) chemical applications. One of the great advantages of this technique is its ability to provide information on the concentration, structure and interaction of biochemical molecules in their microenvironments within intact cells and tissues, non-destructively. Zebrafish (Danio rerio), one of the most important vertebrate model organisms used in developmental biology, are increasingly used in biomedical research, particularly as a model of human disease. In the present work, an attempt is made to study the effect of titanium dioxide, both nano and bulk, on the microenvironment of the liver tissues of Zebrafish using FT-Raman spectroscopy. The results of the present study suggest that TiO₂ exposure demonstrate a marked influence on the microenvironments of the liver tissues of Zebrafish. A shift to a higher wavenumber and an increase in the intensity of the band at ∼1087 cm⁻¹ in the TiO₂ exposed tissues suggest that some of the conformational changes resulting from the alkali recovery process takes place due to TiO₂ exposure. The decreased intensity ratio (I₃₂₂₀/I₃₄₀₀) observed in the titanium-exposed tissues suggests a decreased water domain size, which could be interpreted in terms of weaker hydrogen-bonded molecular species of water in the TiO₂ exposed tissues. The observed shift of COO⁻ bands to higher frequencies shows the disruption of salt bridges as a result of a change in the oppositely charged partners and due to the enhanced random coil conformation. The variation in the intensity ratio of the tyrosyl doublet (I₈₅₈/I₈₂₅) indicates variation in the hydrogen bonding of the phenolic hydroxyl group due to TiO₂ exposure. The results further suggest that the microenvironments are greatly altered due to titanium nano exposure when compared to titanium bulk. In conclusion, the results indicate that FT-Raman spectroscopy might be a useful tool for rapid assessment of nano particle biological interactions.     

Direct equilibration of soil water for delta(18)O analysis and its application to tracer studies

Current methods for stable oxygen isotopic (delta (18)O) analysis of soil water rely on separation of water from the soil matrix before analysis. These separation procedures are not only time consuming and require relatively large samples of soil, but also have been shown to introduce a large potential source of error. Current research at Queen's University Belfast is focused on using direct equilibration of CO(2) with the pore water to eliminate this extraction step using the automated Multiprep system and a Micromass Prism III isotope ratio mass spectrometer (IRMS). The findings of this research indicate the method is less time consuming, more reliable, and reproducible to within accepted limits (+/-0.1% per thousand delta (18)O). In this study the direct equilibration method is used to analyse delta (18)O tracer profiles in the unsaturated zone of field soils, concurrently with chloride tracer profiles, which can be used to assess infiltration rates and mechanisms through the unsaturated zone. Copyright 1999 John Wiley & Sons, Ltd.     

Secondary ion yields produced by keV atomic and polyatomic ion impacts on a self-assembled monolayer surface

A suite of keV polyatomic or 'cluster' projectiles was used to bombard unoxidized and oxidized self-assembled monolayer surfaces. Negative secondary ion yields, collected at the limit of single ion impacts, were measured and compared for both molecular and fragment ions. In contrast to targets that are orders of magnitude thicker than the penetration range of the primary ions, secondary ion yields from polyatomic projectile impacts on self-assembled monolayers show little to no enhancement when compared with monatomic projectiles at the same velocity. This unusual trend is most likely due to the structural arrangement and bonding characteristics of the monolayer molecules with the Au(111). Copyright 1999 John Wiley & Sons, Ltd.