Structure and bonding of aqueous glutamic acid from classical molecular dynamics simulations.

Using classical molecular dynamics we have studied the solution structure of (1:1:29) glutamate with sodium counter ions and water. We provide a structural description of the system, focusing on glutamate­glutamate interactions and providing further insight into glutamate­water interactions. In particular we have characterised the solution structure using three different water potentials, finding little difference between the structural features they predict. We find key differences in the bonding motifs for the two different carboxyl groups, both in the glutamate­glutamate and glutamate­water interactions. Finally, we have examined the hydration structure of the sodium ions in the solution, showing that 10% of the ions are fully hydrated by water, despite the high glutamate concentration.

Solution structure of the aqueous model peptide N-methylacetamide.

Classical molecular dynamics simulations of aqueous N-methylacetamide (NMA) have been performed across a concentration range at 308 K. This peptidic fragment molecule is a useful model for investigating water/peptide hydrogen bond competition. The simulations predict considerable NMA self-association even at low concentrations with a concentration-dependent increase in the ratio of branched to linear clusters. Water-mediated NMA contacts are a feature of this regime, manifested by an unexpected increase in the number of short NMA oxygen contacts arising from water bridge motifs. In contrast, bulk water structure is significantly disrupted by the addition of even small quantities of NMA. With increases in NMA concentration water molecules become progressively more isolated, forming dimers and trimers hydrogen-bonded to NMA. The mixture in this concentration regime may therefore offer a minimal model system for certain structural properties of interior water buried in protein cavities and hydrogen-bonded to mainchain peptide groups.

Adsorption and structure of hydrocarbons in MCM-41: a computational study.

The adsorption of linear, branched, and cyclic hydrocarbons in MCM-41 is studied using Configurational Bias Monte Carlo simulations. A new computational model for MCM-41 is proposed which, although simple, is able to predict adsorption isotherms which are in agreement with the scarce experimental data. The structure of the adsorbed phase is analyzed and found to be similar to that of studies using small, hard spheres trapped in pores. The adsorption of mixtures is investigated, and the adsorption hierarchy is discussed. The structure of the adsorbed mixture is revealed and shows that all components of the mixture exhibit structure, even if they are only adsorbed in small quantities. Finally, the model is modified to include surface roughness and the effect on the adsorption isotherms and structure of the adsorbed phase is discussed.