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Experimental IR spectra in the 500-1850 cm-1 fingerprint frequency range are presented for the isolated, gaseous redox pair ions [Ru(bpy)3]2+, and [Ru(bpy)3]+, where bpy = 2,2'-bipyridine. Spectra are obtained using the FELIX free-electron laser and a quadrupole ion trap mass spectrometer. The 2+ complex is generated by electrospray ionization and the charge-reduced radical cation is produced by gas-phase one-electron reduction in an ion-ion reaction with the fluoranthene radical anion. Experimental spectra are compared against computed spectra predicted by density functional theory (DFT) using different levels of theory. For the closed-shell [Ru(bpy)3]2+ ion, the match between experimental and computed IR spectra is very good; however, this is not the case for the charge-reduced [Ru(bpy)3]+ ion, which demands additional theoretical investigation. When using the hybrid B3LYP functional, we observe that better agreement with experiment is obtained upon reduction of the Hartree-Fock exact-exchange contribution from 204 calculations using the M06 functional appear to be promising in terms of the prediction of IR spectra; however, it is unclear if the correct electronic structure is obtained. The M06 and B3LYP functionals indicate that the added electron in [Ru(bpy)3)]+ is delocalized over the three bpy ligands, while the long-range corrected LC-BLYP and the CAM-B3LYP functionals show it to be more localized on a single bpy ligand. Although these latter levels of theory fail to reproduce the experimentally observed IR frequencies, one may argue that the unusually large bandwidths observed in the spectrum are due to the fluxional character of a complex with the added electron not symmetrically distributed over the ligands. The experimental IR spectra presented here can serve as benchmark for further theoretical investigations.

The infrared multiple-photon dissociation (IRMPD) spectrum of the hexa-coordinated complex of hexacyclen (18-azacrown-6) with Ni2+ shows that the complex has a meridional – and not facial – chelation geometry in the gas phase.

The local structures of DNA and RNA are influenced by protonation, deprotonation and noncovalent interactions with metal cations. In order to determine the effects of sodium cationization on the structures of 2′-deoxycytidine and cytidine, infrared multiple photon dissociation (IRMPD) action spectra of these sodium cationized nucleosides, [dCyd+Na]+ and [Cyd+Na]+, are measured using the FELIX free electron laser and an OPO/OPA laser system. Energy-resolved collision-induced dissociation (ER-CID) experiments for the protonated and sodium cationized forms of the cytosine nucleosides are performed using a Bruker amaZon ETD quadrupole ion trap mass spectrometer (QIT MS) to evaluate the relative propensities of protons and sodium cations for activating the glycosidic bonds of the cytosine nucleosides. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of [dCyd + Na]+ and [Cyd + Na]+. For both cytosine nucleosides, theory suggests that tridentate binding of Na+ to the O2, O4′ and O5′ atoms of the cytosine nucleobase and sugar moiety is the most stable binding mode. However, comparison of the measured IRMPD action spectrum and computed linear IR spectra suggests that anti oriented bidentate conformers of [Cyd + Na]+ are predominantly populated in the experiments. The 2′-hydroxyl substituent of Cyd stabilizes the anti oriented bidentate conformers of [Cyd + Na]+, and enables formation of a 2′OH⋯3′OH hydrogen-bonding interaction. The 2′-hydroxyl substituent is found to stabilize the glycosidic bond of Cyd vs. that of dCyd for both the protonated and sodium cationized cytosine nucleosides. Compared to protonation, sodium cationization activates the N-glycosidic bond less effectively.

We report the fingerprint IR spectra of mass-isolated gaseous coordination complexes of 2,2′-bipyridine (bpy) and 1,4,8,11-tetra-azacyclotetradecane (cyclam) with a copper ion in its I and II oxidation states. Experiments are carried out in a quadrupole ion trap (QIT) mass spectrometer coupled to the FELIX infrared free-electron laser. Dications are prepared using electrospray ionization (ESI), while monocations are generated by charge reduction of the dication using electron transfer-reduction (ETR) in the QIT. Interestingly, [Cu(bpy)2]+ can also be generated directly using ESI, so that its geometries as produced from ETR and ESI can be compared. The effects of charge reduction on the IR spectra are investigated by comparing the experimental spectra with the IR spectra modeled by density functional theory. Reduction of Cu(II) to the closed-shell Cu(I) ion retains the square-planar geometry of the Cu–cyclam complex. In contrast, for the bis–bpy complex with Cu, charge reduction induces a conversion from a near-square-planar to a tetrahedral geometry. The geometry of [Cu(bpy)2]+ is identical to that of the complex generated directly from ESI as a native structure, which indicates that the ETR product ion thermalizes. For [Cu(cyclam)]+, however, the square-planar geometry of the 2+ complex is retained upon charge reduction, although a (distorted) tetrahedral geometry was predicted to be lower in energy. These differences are attributed to different barriers to rearrangement.

Gas-phase infrared multiple-photon dissociation (IRMPD) spectra are recorded for the protonated dye molecules indigo and isoindigo by using a quadrupole ion trap (QIT) mass spectrometer coupled to the free electron laser for infrared experiments (FELIX). From their fingerprint IR spectra (600—1800 cm–1) and comparison with quantum-chemical calculations at the density functional level of theory (B3LYP/6-31++G(d,p)), we derive their structures. We focus particularly on the question of whether trans-to-cis isomerization occurs upon protonation and transfer to the gas phase. The trans-configuration is energetically favored in the neutral forms of the dyes in solution and in the gas phase. Instead, the cis-isomer is lower in energy for the protonated forms of both species, but indigo is also notorious for not undergoing double-bond trans-to-cis isomerization, in contrast to many other conjugated systems. The IR spectra suggest that protoisomerization from trans to cis indeed occurs for both dyes. To estimate the extent of isomerization, on-resonance kinetics are measured on diagnostic and common vibrational frequencies to determine the ratio of cis-to-trans isomers. We find ratios of 65–70% cis and 30–35% trans for indigo versus 75–80% cis and 20–25% trans for isoindigo. Transition-state calculations for the isomerization reactions have been carried out, which indeed suggest a lower barrier for protonated isoindigo, qualitatively explaining the more efficient isomerization.