Tridentate Ionic Hydrogen-Bonding Interactions of the 5-Fluorocytosine Cationic Dimer and Other 5-Fluorocytosine Analogues Characterized by IRMPD Spectroscopy and Electronic Structure Calculations

Abstract

Ionic hydrogen-bonding interactions have been found in several clusters formed by 5-fluorocytosine (5-FC). The chloride and trimethylammonium cluster ions, along with the cationic (proton-bound) dimer have been characterized by infrared multiple-photon dissociation (IRMPD) spectroscopy and electronic structure calculations performed at the B2PLYP/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. IRMPD action spectra, in combination with calculated spectra and relative energetics, indicate that it is most probable that predominantly a single isomer exists in each experiment. For the 5-FC-trimethylammonium cluster specifically, the calculated spectrum of the lowest-energy isomer convincingly matches the experimental spectrum. Interestingly, the cationic dimer of 5-FC was found to have a single energetically relevant isomer (Cationic-IV) involving a tridentate ionic hydrogen-bonding interaction. The three sites of intermolecular ionic hydrogen bonds in this isomer interact very efficiently, leading to a significant calculated binding energy of 180 kJ/mol. The magnitude of the calculated binding energy for this species, in combination with the strong correlation between the simulated and IRMPD spectra, suggests that a tridentate-proton-bound dimer was observed predominantly in the experiments. Comparison of the calculated relative Gibbs free energies (298 K) for this species and several of the other isomers considered also supports the likelihood of the dominant protonated dimer existing as Cationic-IV.

Consecutive Fragmentation Mechanisms of Protonated Ferulic Acid Probed by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations

“…IRMPD, in combination with electronic structure calculations, is a powerful technique for structural elucidation studies such as this . IRMPD spectroscopy experiments were performed at the Centre de Laser Infrarouge d'Orsay (CLIO) and have been described in detail previously [8,12,13,24,31]. The IR-FEL beam was directed into a Bruker (Bruker; 40 Manning Road, Billerica, MA, USA 01821) Esquire 3000+ ion-trap mass spectrometer, equipped with an electrospray ionization interface.…”

“…Relative Gibbs free energies (298 K) are reported in kJ mol −1 Electronic structure calculations have been performed using the Gaussian 09 software package [32]. All geometry optimizations and associated frequency calculations have been performed at the B3LYP/6-311+G(d,p) level of theory, which has been shown to be a reliable protocol, with a good compromise between accuracy and cost, for smaller systems such as those described here [13,14,16,24,[33][34][35][36]. All harmonic frequencies obtained at this level of theory were scaled by 0.9679 [37] in order to compensate for errors arising from the use of a harmonic oscillator approximation in calculating the frequencies, as well as long range electron correlation effects.…”

Assessing the impact of anion–π effects on phenylalanine ion structures using IRMPD spectroscopy

“…[41][42][43][44] This low-cost method efficiently retains the accuracy of the MP2 level of theory by exploiting the reliability and speed of B3LYP/6-311++G(d,p) structural optimizations for small gas-phase ions. [45][46][47] 43-144 unique isomers were considered for each complex that varied according to the halide binding site and the amino acid backbone configuration. Particular care was taken to include Phe ion geometries similar to those previously observed or predicted in the gas phase.…”

The structures and properties of proton- and alkali-bound cysteine dimers

“…While it is tempting, based on these calculated differences, to conclude that isomer 10 is not present in the sample, it is not uncommon in IRMPD spectra to observe transition intensities that are very different from those determined by electronic structure calculations. 12,[25][26][27][28][29] Given the calculated difference in relative energy between isomers 1 and 10, though, we would expect that motif H3 is (at best) a minor contributor to the observed vibrational spectrum. 3.…”