2 research outputs found
Nucleic Acid Bases in Anionic 2′-Deoxyribonucleotides: A DFT/B3LYP Study of Structures, Relative Stability, and Proton Affinities
Protonation of nucleobases in anions
of canonical 2′-deoxyribonucleotides
has been investigated by the DFT computational study at the B3LYP/aug-cc-pvdz
level of theory. It is demonstrated that the protonation leads to
a significant decrease of conformational space of purine nucleotides
while almost all conformers found for non-protonated molecules correspond
to minima of the potential energy surface for protonated mdTMP and
mdCMP. However, in all nucleotides, only one conformer is populated.
This applies to all tautomers of protonated molecules except the mdTMP
and mdCMP with the proton attached to the carbonyl group where a minor
population of second conformer is observed. Protonation of nucleobase
leads to significant elongation of the N-glycosidic bond. These findings
agree well with suggestions that protonation of nucleobase is a first
step in cleavage of the glycosidic bond. The oxygen atoms of both
carbonyl groups of thymine and the N3 atom of the pyrimidine ring
of cytosine, guanine, and adenine represent the most preferable sites
for protonation of anions of 2′-deoxyrobonucleotides. The highest
proton affinity is observed for the base in mdGMP and the lowest for
the thymine moiety in mdTMP. It should be noted that calculated values
of the proton affinities in anionic nucleotides are significantly
higher (by 2–3 eV) than for nucleosides and neutral nucleotides.
This allows assuming that the proton affinity of the base in DNA macromolecule
may be tuned by changing the extent of shielding or neutralization
of negative charge of the phosphate group