The reaction of singlet molecular oxygen with purine DNA bases is investigated by computational means. We support the formation of a transient endoperoxide for guanine and by classical molecular dynamics simulations we demonstrate that the formation of this adduct does not affect the B-helicity. We thus identify the guanine endoperoxide as a key intermediate, confirming a low-temperature nuclear magnetic resonance proof of its existence, and we delineate its degradation pathway, tracing back the preferential formation of 8-oxoguanine versus spiro-derivates in B-DNA. Finally, the latter oxidized 8-oxodGuo product exhibits an almost barrierless reaction profile, and hence is found, coherently with experience, to be much more reactive than guanine itself. On the contrary, in agreement with experimental observations, singlet-oxygen reactivity onto adenine is kinetically blocked by a higher energy transition state.

Oxidatively generated DNA lesions are numerous and versatile, and have been the subject of intensive research since the discovery of 8-oxoguanine in 1984. Even for this prototypical lesion, the precise mechanism of formation remains elusive due to the inherent difficulties in characterizing high-energy intermediates. We have probed the stability of the guanine endoperoxide in B-DNA as a key intermediate and determined a unique activation free energy of around 6 kcal mol(-1) for the formation of the first C-O covalent bond upon the attack of singlet molecular oxygen ((1) O2 ) on the central guanine of a solvated 13 base-pair poly(dG-dC), described by means of quantum mechanics/molecular mechanics (QM/MM) simulations. The B-helix remains stable upon oxidation in spite of the bulky character of the guanine endoperoxide. Our modeling study has revealed the nature of the versatile (1) O2 attack in terms of free energy and shows a sensitivity to electrostatics and solvation as it involves a charge-separated intermediate.

A subbituminous coal and a lignite were treated with some nitrogen reagents in several solvents with the aim of obtaining enriched coal samples which could behave as active carbon precursors. This paper deals with the structural characterization of the samples obtained with urea before and after activation. The attention is focused on the identification of the main functional groups able to react with urea, on the nature of the nitrogen functions introduced in the coal network, and on the behavior of these functions during the activation. The samples were investigated by infrared spectroscopy (DRIFT), X-ray photoelectron spectroscopy (XPS). It was shown that ester/ lactone and carboxylic acid groups are mainly concerned in the reaction with urea, which is solvent dependent. The identification of nitriles proved the occurrence of amides in the first step of the reaction. The participation of ketones, though to a lesser extent, suggests the possibility of further heterocyclization. The nitrogen enrichment of the coals is evidenced by XPS. On the basis of literature data, four nitrogen groups were characterized according to the binding energies. They were assigned to pyrrolic and several pyridinic forms. Their behavior during thermal treatments and steam activation is discussed.