The isomerization of cytosine: Intramolecular hydrogen atom transfer mediated through formic acid

Abstract

The catalytic ability of H 2 O and HCOOH to facilitate the tautomerism of KA to KIt isomer has been studied. It is shown that the direct tautomerism (path A) is unlikely because of the high activation free energy, whereas the presence of H 2 O and HCOOH (paths B and C) significantly contributes to decreasing the activation free energy. Meanwhile, the conventional transition state theory followed by Wigner tunneling correction is applied to estimate the rate constants. The rate constant with Wigner tunneling correction for direct tautomerization is obviously smaller than that of HCOOH-mediated tautomerization, which is the most plausible mechanism. Finally, another important finding is that the ratio of reaction rates between direct tautomerism reaction and catalyst-induced tautomerism increases with the increase of the catalyst concentration at a given temperature. The results of the present study demonstrate the feasibility of acid catalysis for DNA bases isomerization reaction that would otherwise be forbidden.

Tautomer‐Specific Resonant Photoelectron Imaging of Deprotonated Cytosine Anions

“…[1] Other rare tautomers have also been observed by various spectroscopic techniques. [5][6][7][8][9][10][11] Additionally,t he effect of water molecules on the structural dynamics and tautomerism of cytosine have been investigated, [12,13] showing that water can facilitate tautomerization from the canonical form to the rare tautomers by lowering the activation barriers of the prototropic process.T he high stability of the keto-amino tautomers in solution is derived from their large dipole moments. [3,14] Early thermodynamic and kinetic studies showed that the major KAN1H and minor KAN3H forms (Scheme S1 a) are in equilibrium in aqueous solution.…”

Tautomer‐Specific Resonant Photoelectron Imaging of Deprotonated Cytosine Anions

“…Other rare tautomers have also been observed by various spectroscopic techniques . Additionally, the effect of water molecules on the structural dynamics and tautomerism of cytosine have been investigated, showing that water can facilitate tautomerization from the canonical form to the rare tautomers by lowering the activation barriers of the prototropic process. The high stability of the keto–amino tautomers in solution is derived from their large dipole moments .…”

Self‐catalytic mechanism of prebiotic reactions: II. From urea and glycinamide to hypoxanthine

“…The liquid phase of formic acid is similar to that of formamide, consisting of a three‐dimensional NH⋯O hydrogen bond network including different clusters, like dimers, trimers, and tetramers, largely describing the local order of the liquid. [ 18 ] Similar to the formamide molecule, [ 19 ] the formic acid molecule could play the role of a proton shuttle as it has already been demonstrated for the tautomerization reactions of formamide, [ 20 ] cytosine, [ 21 ] and vinyl alcohol and propenol. [ 22 ] Through this way, the formic acid molecule could also act as both a reactant and a catalyst.…”