Molecular dynamics simulations of plastoquinone in solution

Molecular dynamics simulations of plastoquinone, an import ant cofactor in the photosynthetic reaction in green plants, are carried out in water solution. Models of both neutral and anionic plastoquinone are built and thoroughly verified. Detailed information concerning spatial distribution of the hydrogen bonds with coordination numbers, together with rotational energetics of the tail in solution are given. The isoprenoid tail was replaced by an ethyl group, which was found to move freely between 0 degrees (cis to the adjacent carbonyl oxygen) and 90 degrees (perpendicular to the quinone ring plane). The results obtained should remove several inconsistencies between earlier experimental and theoretical results to yield a detailed dynamic picture of plastoquinones in solution. Neutral quinones form only a few weak hydrogen bonds to the solvent molecules, while the anionic forms show a distinct solvation structure due to several strong solute-solvent hydrogen bonds. Both the direction and strength of these hydrogen bonds agree well with recent EPR/ENDOR data.