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The structure of two isomeric stacked dimers of Watson-Crick 9-methyladenine-1-methylthymine pairs was fully optimized using an approximate density functional theory (DFT) method augmented with an empirical dispersion interaction. The results of the calculations reveal that head-to-tail (AT-TA) and head-to-head (AT-AT) dimers possess a significantly different geometry. The structure of both complexes is stabilized by vertical CHÃ¢Â€Â¦O and C-HÃ¢Â€Â¦N hydrogen bonds with the participation of the hydrogen atoms of the methyl groups. The energy of hydrogen bonding and stacking interactions was additionally calculated using the MP2/6-31G*(0.25) method. Differences in the mutual arrangement of the base pairs in two isomeric dimers lead to significant changes of intra and interstrand stacking interaction energies

Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs