SCC-DFTB-D study of intercalating carcinogens: Benzo(a)pyrene and its metabolites complexed with the G-C base pair

The interaction of benzo(a)pyrene (BP) and its metabolites with the GC base pair has been studied using the self-consistent-charge, density functional tight-binding(SCC-DFTB-D) method, augmented by the empirical London dispersion energy term. Structures of the complexes corresponding to a minimum interaction energy obtained using a constrained rigid body search were fully optimized. It is found that the benzylic ring of BP and its anti-conformers is located below the NH2 group of guanine while the syn-conformers exhibit a different binding pattern. The BP triol carbocation (BPTC) in the anti-conformation is stabilized by an additional hydrogen bond between the hydrogen atom of the OH group of BPTC and the N-3 atom of guanine of the G-C base pair. The benzylic ring of BPTC directed toward the minor groove side whereas the pyrenyl ring stacks below the cytosine covering the hydrogen bond region. Guanine bends toward the benzylic ring, making an angle of similar to11-15degrees with the pyrene ring. The calculated equilibrium structures are in good agreement with the available experimental and other theoretical results. (C) 2003 Wiley Periodicals, Inc. Int J Quantum Chem 95: 44 -59, 2003.