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.

In order to simulate the hydrogen bonding and proton transfer (PT) in protein-DNA/RNA interactions, a series of simplified models were employed and investigated in the gas phase. These models included various neutral, anionic and cationic glycine-uracil dimers, and their methylated derivatives generated by the mono- or dimethylation of glycine and/or uracil moieties of the dimer. The results reveal that the only process that can occur in the neutral complexes is a double-PT process leading to proton exchange between the two moieties (i.e., point mutation). The first methyl substitute can reduce the activation energy of the PT process and thus promote the isomerization of the two moieties; further methylation can reduce the isomerization in only some of the cases. In the anionic complexes, only the one-way PT (i.e., amino acid → nucleic acid base) process is energetically favorable, and this PT process is an interesting barrier-free one (BFPT), with the attached electron locating itself at the base moiety. Methylation will disfavor BFPT, but it cannot alter the nature of BFPT. In the cationic complexes, three different PT processes can occur. These processes can transform mutually by adjusting either or both of the methylated sites and methyl number, indicating that the methylation can regulate the dynamics of these PT processes.