Abstract
Basis set effect in evaluation of base pair formation energy of the Watson–Crick type base pair between substituted 1-methyluracil and 9-methyladenine was studied in the Hartree–Fock and second-order Møller–Plesset level of theory. The same trend was observed in the substitution effect in all basis sets attempted; thus, the error depending on the basis set incompleteness is minimal in the evaluation of the substitution effect of the base pair formation energy. Neither the hydrogen bond distance nor the atomic charge was a valid index for the hydrogen bond status in base pairing.
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