Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals.

The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.

The Influence of Metal Ion Binding on the IR Spectra of Nitrogen-Containing PAHs.

Astronomical IR emission spectra form the basis for the now widely accepted abundant presence of polycyclic aromatic hydrocarbons (PAHs) in inter- and circumstellar environments. A small but consistent frequency mismatch is found between the astronomically observed emission band near 6.2 µm and typical CC-stretching vibrations of PAHs measured in laboratory spectra near 6.3-6.4 µm. The shift of the band has been tentatively attributed to a variety of effects, among which the inclusion of heteroatoms, in particular nitrogen, in the PAH skeleton (PANH) as well as to metal ion binding to the PAH molecule. Here we experimentally investigate the combined effect of nitrogen-inclusion and metal ion binding on the IR spectra. In particular, infrared multiple-photon dissociation (IRMPD) spectra are recorded for coordination complexes of Cu+ with one or two quinoline, isoquinoline, and acridine ligands; complexes of the form Cu+(PANH) (MeCN), where the MeCN (acetonitrile) ligand acts as a relatively weakly bound "messenger" are also recorded to qualitatively verify that potential frequency shifts induced by IRMPD are minimal. The experimental IR spectra document the accuracy of IR spectral predictions by density functional theory calculations performed at the B3LYP/6-311+G(2df,2p) level and confirm that a σ-bond is formed between the copper ion and the exoskeletal N atom. The experimental spectra suggest that the CNC stretching mode undergoes a small red shift of up to 20 cm-1, with respect to the band position in the uncomplexed PANH molecule, away from the 6.2 µm interstellar position.