Robin E. Westacott

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.

Water ordering around methane during hydrate formation

The structure of water around methane during hydrate crystallization from aqueous solutions of methane is studied using neutron diffraction with isotopic substitution over the temperature range 18 °C to 4 °C, and at two pressures, 14.5 and 3.4 MPa. The carbon–oxygen pair correlation functions, derived from empirical potential structure refinement of the data, indicate that the hydration sphere around methane in the liquid changes dramatically only once hydrate has formed, with the water shell around methane being about 1 A larger in diameter in the crystal than in the liquid. The methane coordination number in the liquid is around 16±1 water molecules during hydrate formation, which is significantly smaller than the value of 21±1 water molecules found for the case when hydrate is fully formed. Once hydrate starts to form, the hydration shell around methane becomes marginally less ordered compared to that in the solution above the hydrate formation temperature. This suggests that the hydration cage around ...

Full-coordinate free-energy minimisation for complex molecular crystals: type I hydrates

Abstract A method is presented for efficient calculation of free energies for molecular crystals. The method is based on a generalisation of the local harmonic approximation. These calculations are rapid enough to allow optimisation of the free energy with respect to all atomic and crystallographic coordinates at finite temperatures for complex molecular crystals. The procedure has been illustrated for methane hydrate, which has about 150 atoms in the unit cell, and ice Ih. The resulting free energies of the fully optimised structures have been used to predict the conditions for three-phase equilibrium between methane hydrate, ice and methane gas, and shown to give results in excellent agreement with experiment.

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.

Comparison of the Adsorbed Conformation of Barley Lipid Transfer Protein at the Decane−Water and Vacuum−Water Interface: A Molecular Dynamics Simulation

Molecular dynamics simulation is used to model the adsorption of the barley lipid transfer protein (LTP) at the decane-water and vacuum-water interfaces. Adsorption at both surfaces is driven by displacement of water molecules from the interfacial region. LTP adsorbed at the decane surface exhibits significant changes in its tertiary structure, and penetrates a considerable distance into the decane phase. At the vacuum-water interface LTP shows small conformational changes away from its native structure and does not penetrate into the vacuum space. Modification of the conformational stability of LTP by reduction of its four disulphide bonds leads to an increase in conformational entropy of the molecules, which reduces the driving force for adsorption. Evidence for changes in the secondary structure are also observed for native LTP at the decane-water interface and reduced LTP at the vacuum-water interface. In particular, intermittent formation of short (six-residue) regions of beta-sheet is found in these two systems. Formation of interfacial beta-sheet in adsorbed proteins has been observed experimentally, notably in the globular milk protein beta-lactoglobulin and lysozyme.

Dynamics of interfacial reactions between O(3 P) atoms and long-chain liquid hydrocarbons

Recent progress that has been made towards understanding the dynamics of collisions at the gas–liquid interface is summarized briefly. We describe in this context a promising new approach to the experimental study of gas–liquid interfacial reactions that we have introduced. This is based on laser-photolytic production of reactive gas-phase atoms above the liquid surface and laser-spectroscopic probing of the resulting nascent products. This technique is illustrated for reaction of O(3P) atoms at the surface of the long-chain liquid hydrocarbon squalane (2,6,10,15,19,23-hexamethyltetracosane). Laser-induced fluorescence detection of the nascent OH has revealed mechanistically diagnostic correlations between its internal and translational energy distributions. Vibrationally excited OH molecules are able to escape the surface. At least two contributions to the product rotational distributions are identified, confirming and extending previous hypotheses of the participation of both direct and trapping-desorption mechanisms. We speculate briefly on future experimental and theoretical developments that might be necessary to address the many currently unanswered mechanistic questions for this, and other, classes of gas–liquid interfacial reaction.

A local harmonic study of clusters of water and methane

In previous work we have extended the local harmonic model (LHM) to molecular systems and applied it in a study of the bulk properties of gas hydrates. This local molecular harmonic model (LMHM) has several other interesting applications in the study of gas hydrates. In this paper we present one such application: the study of cluster growth towards nucleation. A range of cluster sizes has been studied from 20 to 184 water molecules. Free energy minimisation has been applied using the LMHM and the geometry of the resulting clusters compared to the gas hydrate crystal geometry. Using composite chemical potentials for the solid, gas and interfacial phases a method has been devised to estimate the critical cluster size during nucleation.

Molecular dynamics simulation of the cooperative adsorption of barley lipid transfer protein and cis-isocohumulone at the vacuum-water interface

Molecular dynamic simulations have been carried out on systems containing a mixture of barley lipid transfer protein (LTP) and cis-isocohumulone (a hop derived iso-alpha-acid) in one of its enol forms, in bulk water and at the vacuum-water interface. In solution, the cis-isocohumulone molecules bind to the surface of the LTP molecule. The mechanism of binding appears to be purely hydrophobic in nature via desolvation of the protein surface. Binding of hop acids to the LTP leads to a small change in the 3-D conformation of the protein, but no change in the proportion of secondary structure present in helices, even though there is a significant degree of hop acid binding to the helical regions. At the vacuum-water interface, cis-isocohumulone shows a high surface activity and adsorbs rapidly at the interface. LTP then shows a preference to bind to the preadsorbed hop acid layer at the interface rather than to the bare water-vacuum interface. The free energy of adsorption of LTP at the hop-vacuum-water interface is more favorable than for adsorption at the vacuum-water interface. Our results support the view that hop iso-alpha-acids promote beer foam stability by forming bridges between separate adsorbed protein molecules, thus strengthening the adsorbed protein layer and reducing foam breakdown by lamellar phase drainage. The results also suggest a second mechanism may also occur, whereby the concentration of protein at the interface is increased via enhanced protein adsorption to adsorbed hop acid layers. This too would increase foam stability through its effect on the stabilizing protein layer around the foam bubbles.

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

Thermodynamically, high-pressure (>10s 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.

Separation of dichloromethane-nitrogen mixtures by adsorption: experimental and molecular simulation studies

Experimental and grand canonical Monte Carlo simulation results for the separation of a CH2C12 (1.5 mol%)-N2 binary gas mixture in molecular sieve materials are presented. AlPO4-5 and MCM-41 molecular sieves have been used as the selective adsorbents because they consist of uniform arrays of uni-dimensional channels of micro and meso length scales, respectively. Adsorption isotherms were measured at 318 K and at pressures between 50 kPa and 130 kPa. Two MCM-41 materials have been used, one with a 33 A pore diameter and the other with a 42 Á pore diameter. For AlPO4-5 at 110kPa the total amount adsorbed from experiment was found to be independent of equilibration time at 0.0542, 0.0538 and 0.0547 mmol per g AlPO4-5 for 2, 24 and 48 hours, respectively. However, the selectivity for CH2C12 was found to increase with time from 1.29, to 4.59, to 10.74. For MCM-41 at 110kPa the selectivity for CH2C12 was found to be dependent on pore size. On increasing the pore size from 33 Å to 42 Á the selectivity for CH2C12 increased considerably. Grand canonical Monte Carlo simulations agreed qualitatively with the experimental results, showing a greater selectivity for CH2C12 than for N2. The simulations indicate that MCM-41 has a lower selectivity for CH2C12 than A1PO4-5, which contradicts the experimental results. Reasons for these discrepancies are presented and discussed.