Molecular dynamics simulations of ubiquinone; a survey over torsional potentials and hydrogen bonds

Molecular dynamics simulations, both classical and Car-Parrinello, have bee n carried out to investigate ubiquinone (UQ), a proton mediator in both oxi dative and photo-phosphorylation. The main objectives have been to follow t he dynamics of methoxy groups, conformation of the tail with respect to the ring, hydration and hydrogen bond structure around UQ. The methoxy groups are found to be able to rotate fairly freely. The tail in both UQ and UQ is approximately perpendicular to the ring plane. Only weak hydrogen bonds ar e formed between the neutral form of ubiquinone and water molecules in the solvent, while the anionic form shows a distinct solute-solvent hydrogen bo nd structure. We also conclude that anionic UQ can be accurately modelled b y molecular mechanics methods, but the conformation of the methoxy groups i n neutral UQ can hardly be properly modelled using a standard force field.