Alkali metal cation binding affinities of cytosine in the gas phase: revisited

Abstract

Binding of metal cations to the nucleobases can influence base pairing, base stacking and nucleobase tautomerism. Gas-phase condensation of dc discharge generated alkali metal cations and thermally vaporized cytosine (DC/FT) has been found to produce kinetically trapped excited tautomeric conformations of the M(+)(cytosine) complexes, which influences the threshold collision-induced dissociation (TCID) behavior. In order to elucidate the effects of the size of alkali metal cation on the strength of binding to the canonical form of cytosine, the binding affinities of Na(+) and K(+) to cytosine are re-examined here, and studies are extended to include Rb(+) and Cs(+) again using TCID techniques. The M(+)(cytosine) complexes are generated in an electrospray ionization source, which has been shown to produce ground-state tautomeric conformations of M(+)(cytosine). The energy-dependent cross sections are interpreted to yield bond dissociation energies (BDEs) using an analysis that includes consideration of unimolecular decay rates, the kinetic and internal energy distributions of the reactants, and multiple M(+)(cytosine)-Xe collisions. Revised BDEs for the Na(+)(cytosine) and K(+)(cytosine) complexes exceed those previously measured by 31.9 and 25.5 kJ mol(-1), respectively, consistent with the hypothesis proposed by Yang and Rodgers that excited tautomeric conformations are accessed when the complexes are generated by DC/FT ionization. Experimentally measured BDEs are compared to theoretical values calculated at the B3LYP and MP2(full) levels of theory using the 6-311+G(2d,2p)_HW* and def2-TZVPPD basis sets. The B3LYP/def2-TZVPPD level of theory is found to provide the best agreement with the measured BDEs, suggesting that this level of theory can be employed to provide reliable energetics for similar metal-ligand systems.

Cationic Noncovalent Interactions: Energetics and Periodic Trends

“…Uncertainties in parentheses. A = adenine, C = cytosine, G = guanine, T = thymine, U = uracil; m = methyl, f = fluorine, br = bromine, cl = chlorine, i = iodine, S = sulfur; superscripts indicate the position of substitution. b C = threshold collision-induced dissociation; − K = kinetic method c Values reanchored, adjusted from 298 to 0 K, and adjusted for propagation of error as described in the text. d Values for O2N3 binding to the C1 canonical tautomer of C. e Values for N1O2 binding to the C3 tautomer of C. …”

“…TCID studies (C) provide absolute affinities for the same three alkali metal cations bound to A, C, U, and T, − but not to G. Notably the cytosine system has been examined twice, originally using a flow tube ion source in which kinetically trapped excited tautomers of the M + (C) complexes are formed (as identified by comparison with theory) and then using an electrospray source that generates the ground tautomer . In the earlier work, the values obtained correspond to metal binding to the N1 and O2 positions of the C 3 tautomer of cytosine in which the hydrogen on N1 has shifted to O2.…”

Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNAi-Motif

“…The threshold regions of the measured CID cross-sections are modeled using procedures developed elsewhere [55][56][57][58][59][60][61][62] that have been found to reproduce CID cross-sections well [63][64][65][66][67]. Details regarding data handling and analysis procedures, which includes explicitly accounting for the internal and translational energy distributions of the reactant proton-bound dimers, the effects of multiple ion-neutral collisions, and the lifetime of the dissociating proton-bound dimers, are summarized in the Supplementary Information.…”

Photoelectron spectroscopy of solvated dicarboxylate and alkali metal ion clusters, M+[O2C(CH2)2CO2]2−[H2O]n(M = Na, K;n= 1–6)

“…We tentatively assign it to higher energy quaternary [Na + , HDC 2 − , OH − , H 2 O] complex, hinging on the hypothesis that such complex may be kinetic trapped. [35][36][37][38][39]…”

“…However, it needs to be pointed out that all component ions in both quaternary and ternary complexes [Na + , HDC 2 − , OH − , H 2 O, DC 2 2− ] exist in our sprayed solution, and previous studies have shown that higher energy isomers can often exist even at low temperatures due to kinetic trapping. [35][36][37][38][39] Therefore the existence of such quaternary system remains a possibility, which may contribute to the weak low binding energy band.…”