The adenine–thymine base pair was studied in the presence of hydroxyl radicals in order to probe the hydrogen bond effect.The results show that the hydrogen bonds have little effect on the hydroxylation and dehydrogenation happened at the sites,which are not involved in a hydrogen bond,while at the sites involved in hydrogen bond formation in the base pair,the reaction becomes more difficult,both in view of the free energy barrier and the exothermicity.With a 6-311++G(d,p)level of description,both B3LYP and MP2 methods confirm that the C8 site of isolated adenine has the highest possibility to form covalent bond with the hydroxyl radicals,though with different energetics:B3LYP predicts a barrierless pathway,while MP2 finds a transition state with an energy of 106.1 kJ/mol.For the dehydrogenation reactions,B3LYP method predicts that the free energy barrier increases in the order of HN9