Journal of Physical Chemistry A, Vol.110, No.12, 4180-4187, 2006
Fluorobenzene-nucleobase interactions: Hydrogen bonding or pi-stacking?
Studies on modified DNA oligomers and polymerase reactions have previously demonstrated that canonical nucleobases can exhibit stable and even selective pairing with shape-complementary fluorobenzene nucleotides. Because of the fluorination of the pairing edges, hydrogen bonds are believed to be absent, and the local DNA stability has been attributed to pi-stacking and shape complementarity. Using two-color resonant two-photon ionization and fluorescence emission spectroscopies, we show here that supersonically cooled complexes of the nucleobase analogue 2-pyridone with seven substituted fluorobenzenes (1-fluorobenzene, 1,2- and 1,4-difluorobenzene, 1,3,5-and 1,2,3-trifluorobenzene, 1,2,4.5- and 1,2,3,4-tetrafluorobenzene) are hydrogen-bonded and not pi-stacked. The S-1 <-> S-0 vibronic spectra show intermolecular vibrational frequencies that are characteristic for doubly hydrogen bonded complexes. The bands shift to the blue with increasing 0 hydrogen-bond strength; the measured spectral blue shifts delta v are in excellent agreement with the ab initio calculated shifts. The spectral shifts are also linearly correlated with the calculated hydrogen-bond dissociation energies Do, published in a companion paper (Frey, J. A.; Leist, R.; Leutwyler, S. J. Phys. Chem. A 2006, 110, 4188). This correlation allows us to reliably estimate the ground-state dissociation energies as Do 6 kcal/mol of the 2-pyridone-fluorobenzene complexes from the observed spectral shifts.