Hydrogen Bonding of the Nucleobase Mimic 2-Pyridone to Fluorobenzenes: An ab Initio Investigation

Water bridges anchored by a C–H⋯O hydrogen bond: the role of weak interactions in molecular solvation

Hydrogen-bonded water bridges are re-directed from a polar NH bond to a weakly activated C(2)–H bond upon N-methylation. Infrared spectra, supported by ab initio calculations, provide direct evidence of the role of the C(2)–H donor in the solvation of the imidazole ring.

Thieno analogues of RNA nucleosides: a detailed theoretical study

We use first-principles density functional theory calculations to investigate the structural, energetic, bonding aspects, and optical properties of recently synthesized thieno-analogues of RNA nucleosides. The results are compared against the findings obtained for both the natural nucleosides as well as available experimental data. We find that the modified nucleosides form the hydrogen bonded Watson-Crick (WC) base pairing with similar H-bonding energy as obtained for the natural nucleosides. We have calculated and compared the charge transfer integrals for the H-bonded natural and thieno-modified nucleosides. We find that the thieno modification of these nucleosides strongly affects the charge transfer integrals due to the difference in extent of orbital delocalization in these two types of nucleosides. We also find that the degree of reduction of charge transfer integrals is larger for the H-bonded A-U pair than in the G-C pair. We also focus on the optical absorption properties of these thieno-modified nucleosides and their WC H-bonded base pairs in gas phase as well as with implicit water. Our calculated results show that the low energy peaks in the absorption spectra mainly arise because of the π-π* electronic transition for both the nucleosides, and the observed red shift for thieno-nucleosides compared to natural nucleosides are consistent with the calculated decrease in electronic gaps. Our results demonstrate that the thieno modification of natural nucleosides significantly modifies their electronic and optical properties, although the basic structural and bonding aspects remained the same. It also gives a microscopic understanding of the experimentally observed optical behaviors.

Energetically important C-H···F-C pseudohydrogen bonding in water: evidence and application to rational design of oligonucleotides with high binding affinity

It is controversial whether organic fluorine can form energetically important hydrogen bonds in aqueous environments. We previously showed by NMR and molecular modeling that the unexpectedly high binding affinity of 2'F-ANA is largely due to a C-H···F-C pseudohydrogen bond at pyrimidine-purine steps. Comparisons of the melting of duplexes with identical sequence composition but a rearranged sequence confirm that energetically important fluorine-mediated pseudohydrogen bonding is in operation in these sequences. The effect is of particular importance when the H-bond donor (purine H8) is activated by the presence of fluorine at its own 2'-position. These results provide a rational method to increase the binding affinity of antisense oligonucleotides by placement of 2'F-ANA modifications at pyrimidine-purine steps.

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.

A peptide co-solvent under scrutiny: self-aggregation of 2,2,2-trifluoroethanol

Trifluoroethanol (TFE) and its aggregates are studied via supersonic jet FTIR and Raman spectroscopy as well as by quantum chemistry and simple force field approaches. A multi-slit nozzle is introduced to study collisionally excited clusters. Efforts are made to extract harmonic frequencies from experiment for better comparison to theory. Based on deuteration, the OH stretching anharmonicity changes weakly upon dimerization, but increases for trimers. Among the possible dimer conformations, only an all-gauche, homoconfigurational, compact, OH-F connected structure is observed in an extreme case of chiral discrimination. Quantum tunneling assisted pathways for this surprising helicity synchronization are postulated. The oscillator coupling in hydrogen-bonded trimers is analyzed. Trans conformations of TFE start to become important for trimers and probably persist in the liquid state. Simple force fields can be refined to capture some molecular recognition features of TFE dimer, but their limitations are emphasized.

An ab Initio Benchmark Study of Hydrogen Bonded Formamide Dimers

The five singly and doubly hydrogen bonded dimers of formamide are calculated at the correlated level by using resolution of identity Møller-Plesset second-order perturbation theory (RIMP2) and the coupled cluster with singles, doubles, and perturbative triples [CCSD(T)] method. All structures are optimized with the Dunning aug-cc-pVTZ and aug-cc-pVQZ basis sets. The binding energies are extrapolated to the complete basis set (CBS) limit by using the aug-cc-pVXZ (X = D, T, Q) basis set series. The effect of extending the basis set to aug-cc-pV5Z on the geometries and binding energies is studied for the centrosymmetric doubly N-H...O bonded dimer FA1 and the doubly C-H...O bonded dimer FA5. The MP2 CBS limits range from -5.19 kcal/mol for FA5 to -14.80 kcal/mol for the FA1 dimer. The DeltaCCSD(T) corrections to the MP2 CBS limit binding energies calculated with the 6-31+G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are mutually consistent to within < or =0.03 kcal/mol. The DeltaCCSD(T) correction increases the binding energy of the C-H...O bonded FA5 dimer by 0.4 kcal/mol or approximately 9% over the distance range +/-0.5 Angstrom relative to the potential minimum. This implies that the ubiquitous long-range C-H...O interactions in proteins are stronger than hitherto calculated.

2-pyridone: The role of out-of-plane vibrations on the S1↔S0 spectra and S1 state reactivity

The S(1)<-->S(0) vibronic spectra of supersonic jet-cooled 2-pyridone [pyridin-2-one (2PY)] and its N-H deuterated isotopomer (d-2PY) have been recorded by two-color resonant two-photon ionization, laser-induced fluorescence and emission, and fluorescence depletion spectroscopies. By combining these methods, the B origin of 2PY at 0(0) (0)+98 cm(-1) and the bands at +218 and +252 cm(-1) are identified as overtones of the S(1) state out-of-plane vibrations nu(1) (') and nu(2) ('), as are the analogous bands of d-2PY. Anharmonic double-minimum potentials are derived for the respective out-of-plane coordinates that predict further nu(1) (') and nu(2) (') overtones and combinations, reproducing approximately 80% of the vibronic bands up to 600 cm(-1) above the 0(0) (0) band. The fluorescence spectra excited at the electronic origins and the nu(1) (') and nu(2) (') out-of-plane overtone levels confirm these assignments. The S(1) nonplanar minima and S(1)<--S(0) out-of-plane progressions are in agreement with the determination of nonplanar vibrationally averaged geometries for the 0(0) (0) and 0(0) (0)+98 cm(-1) upper states by Held et al. [J. Chem. Phys. 95, 8732 (1991)]. The fluorescence lifetimes of the S(1) state vibrations show strong mode dependence: Those of the out-of-plane levels decrease rapidly above 200 cm(-1) excess vibrational energy, while the in-plane vibrations nu(5) ('), nu(8) ('), and nu(9) (') have longer lifetimes, although they are above or interspersed with the "dark" out-of-plane states. This is interpreted in terms of an S(1) (') state reaction with a low barrier towards a conical intersection with a prefulvenic geometry. Out-of-plane vibrational states can directly surmount this barrier, whereas in-plane vibrations are much less efficient in this respect. Analysis of the fluorescence spectra allows to identify nine in-plane S(0) (') state fundamentals, overtones of the S(0) state nu(1) (") and nu(2) (") out-of-plane vibrations, and >30 other overtones and combination bands. The B3LYP6-311++G(d,p) calculated anharmonic wave numbers are in very good agreement with the observed fundamentals, overtones, and combinations, with a deviation Delta(rms)=1.3%.

The difluorotoluene debate--a decade later

2,4-Difluorotoluene is unusual among hydrofluorocarbons because it is shaped like the DNA base thymine. It was first synthesised as a nucleotide analogue and incorporated into DNA a decade ago. Although it is a nonpolar molecule, it was found to be replicated by DNA polymerase enzymes as if it were thymine. We concluded that replication of DNA base pairs can occur without Watson-Crick hydrogen bonds, and hypothesised that steric effects, rather than these hydrogen bonds, were the main arbiters of DNA replication fidelity. A debate was initiated then, with claims by some that the molecule is polar and forms hydrogen bonds with adenine, thus supporting the hydrogen bonding theory of DNA replication. Here we discuss the evolution of this debate, and reflect on the relevant data that have since come from hundreds of papers and dozens of laboratories. Although discussion on this topic continues, the steric hypothesis for DNA replication is now widely accepted among biochemists, and the changing paradigm has been reflected in textbooks.

Quantitative chirality synchronization in trifluoroethanol dimers

2,2,2-Trifluoroethanol molecules synchronize their transiently chiral gauche configurations upon dimerization in supersonic jet expansions, while they avoid an energetically competitive heteroconfigurational hydrogen bonded dimer topology predicted by extensive quantum chemical calculations.