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 S1 <--> S0 vibronic spectra show intermolecular vibrational frequencies that are characteristic for doubly hydrogen bonded complexes. The bands shift to the blue with increasing hydrogen-bond strength; the measured spectral blue shifts deltanu are in excellent agreement with the ab initio calculated shifts. The spectral shifts are also linearly correlated with the calculated hydrogen-bond dissociation energies D0, 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 D0 approximately 6 kcal/mol of the 2-pyridone.fluorobenzene complexes from the observed spectral shifts.
Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
Roman
R
Leist
Jann A
JA
Frey
Samuel
S
Leutwyler
D005464:Fluorobenzenes / Q000737:chemistry*; D006860:Hydrogen Bonding; D015394:Molecular Structure; D009705:Nucleosides / Q000737:chemistry*; D011728:Pyridones / Q000737:chemistry; D011789:Quantum Theory; D012680:Sensitivity and Specificity; D013050:Spectrometry, Fluorescence / Q000379:methods; D013237:Stereoisomerism
D005464:Fluorobenzenes; D009705:Nucleosides; D011728:Pyridones