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The solution conformation of peptides rich in the alpha, alpha-dialkylated amino acid Aib has proven to be a subtle problem, not because of helix/coil transitions, but rather because of alpha-helical/3(10)-helical competition. A special series of peptides containing 75% Aib has been synthesized that feature identical amino acid composition but differing sequences; they are sequence permutation isomers. Nuclear magnetic resonance hydrogen-bonding studies reveal that there is a sequence permutation induced transition between the two alternative helical forms within this set. The implications for the design and conformational prediction of helical Aib-rich peptides are discussed.

Constant temperature and constant pressure molecular dynamics calculations have been performed on the extended simple point charge (SPC/E) model water to understand the effects of pressure on its structural and dynamical properties. The effect of pressure is to increase the presence of interstitial water molecules, which is shown to be responsible for the experimentally observed increase in the first x-ray diffraction peak and a broadening of the OOO∧ bond angle distribution. These structural changes lead to weaker hydrogen bonding and the observed minimum in the rotational correlation time as a function of pressure. The weak maximum in the measured translational diffusion coefficient at around 1.5 kbar was not reproduced. The temperature of the density maximum was estimated to occur at 245±4 K, which suggests that structural changes with increasing pressure and decreasing temperature are not quantitatively reproduced by the SPC/E model.

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State-of-the-art molecular dynamics (MD) methods are employed to study the properties of linear and branched fluid alkanes in bulk and at solid/fluid interfaces. The fluids are modelled with a transferable intermolecular potential, whose effectiveness is demonstrated through calculations of the shear viscosity using equilibrium and non-equilibrium techniques. Monolayer and multilayer films of linear and branched alkanes, on both metal and graphite surfaces, are studied to understand the effects of molecular architecture on the adsorption behaviour of these molecules. Preferential adsorption of a component in a mixture of linear and branched alkanes is also investigated. The parameters characterizing the hydrodynamic boundary conditions of confined liquid alkanes under shear flow are determined using linear response theory and non-equilibrium molecular dynamics (NEMD) simulations. The agreement between the present simulations on fluid alkanes and available experimental data is excellent.