Inelastic scattering of OH radicals from organic liquids: isolating the thermal desorption channel.

Inelastic scattering of OH radicals from liquid surfaces has been investigated experimentally. An initially translationally and rotationally hot distribution of OH was generated by 193 nm photolysis of allyl alcohol. These radicals were scattered from an inert reference liquid, perfluorinated polyether (PFPE), and from the potentially reactive hydrocarbon liquids squalane (C30H62, 2,6,10,15,19,23-hexamethyltetracosane) and squalene (C30H50, trans-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene). The scattered OH v = 0 products were detected by laser-induced fluorescence. Strong correlations were observed between the translational and rotational energies of the products. The high-N levels are translationally hot, consistent with a predominantly direct, impulsive scattering mechanism. Impulsive scattering also populates the lower-N levels, but a component of translationally relaxed OH, with thermal-desorption characteristics, can also be seen clearly for all three liquids. More of this translationally and rotationally relaxed OH survives from squalane than from squalene. Realistic molecular dynamics simulations confirm that double-bond sites are accessible at the squalene surface. This supports the proposition that relaxed OH may be lost on squalene via an addition mechanism.

The interface between water and a hydrophobic gas.

Classical molecular dynamics simulations have been performed to investigate the interface between liquid water and methane gas under methane hydrate forming conditions. The local environments of the water molecules were studied using order parameters which distinguish between liquid water, ice and methane hydrate phases. Bulk water and water/air interfaces were also studied to allow comparisons to be made between water molecules in the different environments and to determine the effects of the different methane densities studied. Good agreement between experimental and calculated surface tensions is obtained if long range corrections are included. The water surface is found to have a structure which is very similar to that of bulk water, but more tetrahedral, and more clathrate-like than ice-like. In these simulations the concentration of methane in water at the interface is shown to be appropriate for clathrates at higher gas densities (pressures). The orientation of water molecules around methane molecules in the interfacial region appears to depend only weakly on pressure and one of the difficulties in forming hydrate is the availability of water molecules tangential to the hydrate cage. At the interface, the water structure is more disordered than in the bulk water region with increased occurrence compared with the bulk of those angles and orientations found in the clathrate structure.

Molecular dynamics study to identify the reactive sites of a liquid squalane surface.

Molecular dynamics simulations of liquid squalane, C30H62, were performed, focusing in particular on the liquid-vacuum interface. These theoretical studies were aimed at identifying potentially reactive sites on the surface, knowledge of which is important for a number of inelastic and reactive scattering experiments. A united atom force field (Martin, M. G.; Siepmann, J. I. J. Phys. Chem. B 1999, 103, 4508-4517) was used, and the simulations were analyzed with respect to their interfacial properties. A modest but clearly identifiable preference for methyl groups to protrude into the vacuum has been found at lower temperatures. This effect decreases when going to higher temperatures. Additional simulations tracking the flight paths of projectiles directed at a number of randomly chosen surfaces extracted from the molecular dynamics simulations were performed. The geometrical parameters for these calculations were chosen to imitate a typical abstraction reaction, such as the reaction between ground-state oxygen atoms and hydrocarbons. Despite the preference for methyl groups to protrude further into the vacuum, Monte Carlo tracking simulations suggest, on geometric grounds, that primary and secondary hydrogen atoms are roughly equally likely to react with incoming gas-phase atoms. These geometric simulations also indicate that a substantial fraction of the scattered products is likely to undergo at least one secondary collision with hydrocarbon side chains. These results help to interpret the outcome of previous measurements of the internal and external energy distribution of the gas-phase OH products of the interfacial reaction between oxygen atoms and liquid squalane.

Search for memory effects in methane hydrate: structure of water before hydrate formation and after hydrate decomposition.

Neutron diffraction with HD isotope substitution has been used to study the formation and decomposition of the methane clathrate hydrate. Using this atomistic technique coupled with simultaneous gas consumption measurements, we have successfully tracked the formation of the sI methane hydrate from a water/gas mixture and then the subsequent decomposition of the hydrate from initiation to completion. These studies demonstrate that the application of neutron diffraction with simultaneous gas consumption measurements provides a powerful method for studying the clathrate hydrate crystal growth and decomposition. We have also used neutron diffraction to examine the water structure before the hydrate growth and after the hydrate decomposition. From the neutron-scattering curves and the empirical potential structure refinement analysis of the data, we find that there is no significant difference between the structure of water before the hydrate formation and the structure of water after the hydrate decomposition. Nor is there any significant change to the methane hydration shell. These results are discussed in the context of widely held views on the existence of memory effects after the hydrate decomposition.

Piezotolerance as a metabolic engineering tool for the biosynthesis of natural products.

Thermodynamically, high-pressure (>10's of MPa) has a potentially vastly superior effect on reactions and their rates within metabolic processes than temperature. Thus, it might be expected that changes in the pressure experienced by living organisms would have effects on the products of their metabolism. To examine the potential for modification of metabolic pathways based on thermodynamic principles we have performed simple molecular dynamics simulations, in vacuo and in aquo on the metabolites synthesized by recombinant polyketide synthases (PKS). We were able to determine, in this in silico study, the volume changes associated with each reaction step along the parallel PKS pathways. Results indicate the importance of explicitly including the solvent in the simulations. Furthermore, the addition of solvent and high pressure reveals that high pressure may have a beneficial effect on certain pathways over others. Thus, the future looks bright for pressure driven novel secondary metabolite discoveries, and their sustained and efficient production via metabolic engineering.