Modeling platinum group metal complexes in aqueous solution.

We construct force fields suited for the study of three platinum group metals (PGM) as chloranions in aqueous solution from quantum chemical computations and report experimental data. Density functional theory (DFT) using the local density approximation (LDA), as well as extended basis sets that incorporate relativistic corrections for the transition metal atoms, has been used to obtain equilibrium geometries, harmonic vibrational frequencies, and atomic charges for the complexes. We found that DFT calculations of [PtCl(6)](2-).3H(2)O, [PdCl(4)](2-).2H(2)O, and [RhCl(6)](3-).3H(2)O water clusters compared well with molecular mechanics (MM) calculations using the specific force field developed here. The force field performed equally well in condensed phase simulations. A 500 ps molecular dynamics (MD) simulation of [PtCl(6)](2-) in water was used to study the structure of the solvation shell around the anion. The resulting data were compared to an experimental radial distribution function derived from X-ray diffraction experiments. We found the calculated pair correlation functions (PCF) for hexachloroplatinate to be in good agreement with experiment and were able to use the simulation results to identify and resolve two water-anion peaks in the experimental spectrum.

Molecular dynamics simulations of the N-linked oligosaccharide of the lectin from Erythrina corallodendron.

Molecular dynamics simulations have been used to model the flexibility of the seven-sugar oligosaccharide of the lectin from Erythrina corallodendron in three separate simulations: one of the isolated oligosaccharide in vacuo, one of the oligosaccharide in solution and one of the oligosaccharide linked to the protein in solution. Adiabatic conformational energy maps were prepared for each of the disaccharide linkages as a means of interpreting the observed dynamics and conformational averages in terms of intramolecular energy. The inclusion of aqueous solvent molecules appears to be necessary to reproduce the experimental conformational behavior, which also cannot be predicted well from conformational energy maps for the disaccharide linkages alone. The crystallographically determined conformation does not appear to be induced by the crystal dimerization, but is rather stable in solution. The build-up of fluctuations along the successive linkages of the oligosaccharide is significant and would be sufficient to prevent branch residues from being located in most crystal structure determinations. Good general agreement between the calculated solution structure and the average structure determined by NMR was found for most of the oligosaccharide linkages.