A theoretical prediction on the ground‐state complexes bound by metal ions to thymine base isomers

Abstract

Stability orderings of 150 stable complexes formed by metal ions (Na+, K+, Ca2+, Mg2+, and Zn2+) and 13 stable thymine tautomers in both solvent and gas phases are obtained, and the optimal binding site for a metal ion in a specific thymine tautomer is identified. Results indicate that the complex with the canonical thymine tautomer (T1) is more stable than those with the rare ones, and the monodentate complex M–T1o4(o2) are their ground‐state form in the solvent phase. The ground‐state thymine complexes bound by Ca2+, Mg2+, or Zn2+ become bidentate M–T3o4lo2,n3, which is derived from a rare thymine tautomer T3o4l, whereas those bound by Na+ and K+ are still monodentate complexes M–T1o4(o2), however, in the gas phase. The differences in stability are discussed in detail from the binding strength of metal ions, relative energy of the corresponding thymine tautomers, and solution effect. Copyright © 2011 John Wiley & Sons, Ltd.

Tautomerisation of thymine acts against the Hückel 4N + 2 rule. The effect of metal ions and H-bond complexations on the electronic structure of thymine

“…In agreement with previous studies, 23,38 the most stable complexes of thymine tautomers with metal ions are found for thy1, where the cation interacts with the O10 atom of the carbonyl group (M + ⋯O10). The decrease of thymine complexes stability up to E rel = 10 kcal mol −1 (Table S6 ‡) occurs in the following sequence: M + ⋯N3,O8 of thy3, M + ⋯O8 of thy1 and M + ⋯O10 of thy2.…”

“…Thymine is a six-membered heterocyclic molecule which can exist in the form of 13 tautomers/rotamers. The 1H,3Hdiketo tautomer, which contains two CvO groups and two N-H groups constituting inherent parts of the ring, is the most stable in the gas phase, solution and the solid state 19,20 which was confirmed by a series of theoretical [21][22][23] and experimental † Dedicated to our friend, Professor Jacek Lipkowski of Guelph University, on the occasion of his 70 th birthday.…”

“…32 Metal cations contribute to the stabilization of rare nucleobase tautomers 23,33 and increase the probability of gene mutations. [34][35][36] Such interactions of thymine with alkali metal ions are well described by theoretical 23,[37][38][39] and experimental [40][41][42][43] methods. It was found that metal cations in all types of complexes studied preferentially bind to the oxygen at the C4 atom of thymine as well as in uracil.…”

“…31 Another factor which can cause a mismatch in the base pairing is the metalation of nucleobases. 32 Metal cations contribute to the stabilization of rare nucleobase tautomers 23,33 and increase the probability of gene mutations. [34][35][36] Such interactions of thymine with alkali metal ions are well described by theoretical 23,[37][38][39] and experimental [40][41][42][43] methods.…”

Effect of Alkali Metal Cations on Length and Strength of Hydrogen Bonds in DNA Base Pairs

“…For divalent cations, it has been experimentally shown that the coordination at the N7 position of adenine is preferred, whereas for Ag + , the coordination occurs at N3 and N7 of adenine . The bases thymine and uracil bind the metal cations at O4 atom . For guanine and cytosine, the coordination with cation is bifurcated, that is, the metal cation is bound to the N7 and O6 atoms of guanine and the N3 and O2 atoms of cytosine, respectively.…”