Benzo[a]pyrene and benz[c]phenanthrene: the effect of structure on the binding of water molecules to the diol epoxides.
The interactions with water of the diol epoxides (DEs) of both a planar and a nonplanar PAH have been examined using molecular dynamics. To determine probable water locations around the DE for later use in the study of DE protonation, molecular dynamics simulations using the OPLS force field were carried out on diol epoxides surrounded by a 22 A box of explicit water molecules. Results for 30 ps simulations indicate that 10-60% of the time, depending strongly on the conformation and type of the DE, there is a water molecule forming a hydrogen bond with the epoxide oxygen. The patterns seen in the frequency at which a DE binds a water molecule reflect patterns seen in the relationship between the type of PAH DE and amount of DNA adduct formation. Examination of the orientations and arrangements of the water and DEs during the simulations showed that the bound waters existed in several preferred configurations which are also dependent upon the PAH DE geometry.
Brown
Katrina W
KW
United States Environmental Protection Agency, NHEERL/ECD, Research Triangle Park, NC 27711, USA.
Little
Stephen B
SB
Rabinowitz
James R
JR
D001564:Benzo(a)pyrene / Q000737:chemistry*; D001665:Binding Sites; D003198:Computer Simulation; D004852:Epoxy Compounds / Q000737:chemistry*; D008968:Molecular Conformation; D010616:Phenanthrenes / Q000737:chemistry*; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry*
D004852:Epoxy Compounds; D010616:Phenanthrenes; D014867:Water; D001564:Benzo(a)pyrene; C002615:benzo(c)phenanthrene