Infrared Spectrum of the Ag⁺–(Pyridine)₂ Ionic Complex: Probing Interactions in Artificial Metal‐Mediated Base Pairing

Abstract

The isolated pyridine-Ag(+)-pyridine unit (Py-Ag(+)-Py) is employed as a model system to characterize the recently observed Ag(+)-mediated base pairing in DNA oligonucleotides at the molecular level. The structure and infrared (IR) spectrum of the Ag(+)-Py(2) cationic complex are investigated in the gas phase by IR multiple-photon dissociation (IRMPD) spectroscopy and quantum chemical calculations to determine the preferred metal-ion binding site and other salient properties of the potential-energy surface. The IRMPD spectrum has been obtained in the 840-1720 cm(-1) fingerprint region by coupling the IR free electron laser at the Centre Laser Infrarouge d'Orsay (CLIO) with a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with an electrospray ionization source. The spectroscopic results are interpreted with quantum chemical calculations conducted at the B3LYP/aug-cc-pVDZ level. The analysis of the IRMPD spectrum is consistent with a σ complex, in which the Ag(+) ion binds to the nitrogen lone pairs of the two Py ligands in a linear configuration. The binding motif of Py-Ag(+)-Py in the gas phase is the same as that observed in Ag(+)-mediated base pairing in solution. Ag(+) bonding to the π-electron system of the aromatic ring is predicted to be a substantially less-favorable binding motif.

On the Ag+–cytosine interaction: the effect of microhydration probed by IR optical spectroscopy and density functional theory

“…This common feature between the mentioned structures is expected given that Ag + is well known to preferentially form di-ligated complex through linear coordination 46,47. In the [CAg-H 2 O] + -2 isomer, the Ag + cation is bound to the carbonyl oxygen of cytosine and the water oxygen, and the O-Ag + -O angle is predicted to be 180°.…”

Infrared spectroscopy of copper-resveratrol complexes: A joint experimental and theoretical study

“…At the same time the observed analogies seem to suggest a comparable perturbation of neutral resveratrol upon binding of [Cu(Resv)] + as well as upon ionization by electron loss. The present investigation may open the way to a systematic investigation of charged complexes of transition metals with bioactive molecules in an isolated state, 10,[36][37][38][39][40][41][42][43][44] hopefully contributing to elucidate the factors governing their biological function.…”

IRMPD spectroscopy of metalated flavins: structure and bonding of Mq+–lumichrome complexes (Mq+ = Li+–Cs+, Ag+, Mg2+)

“…42 Such orbital interactions have previously been analysed for Ag + binding to pyridine, phenol, and polycyclic aromatic hydrocarbons via IR(M)PD spectra and quantum chemical calculations. 29,30,32 As the calculated ionization energy of LC (IE = 7.99 eV) is slightly higher than that of Ag (IE = 7.58 eV), 41 the charge in [AgLC] + complexes is mostly localized on the metal atom, justifying the Ag + LC notation. Because of the similar IE values of Ag and LC, charge transfer interaction involving the p HOMO of LC may stabilize p complexes of Ag + LC relative to the s complexes.…”

“…This combined strategy has proven to be a powerful tool to characterize metal ion complexes of a large variety of (bio-)molecules. [21][22][23][24][25][26][27][28][29][30][31][32][33] Similar to protonated flavins, 18 the CO stretch modes serve as the main indicator of the metal binding sites. The comparison of the measured IRMPD spectra with the calculated linear absorption spectra provides insight into their respective structures and bonding mechanisms.…”