J. Sponer et P. Hobza, NONPLANAR GEOMETRIES OF DNA BASES - AB-INITIO 2ND-ORDER MOLLER-PLESSET STUDY, Journal of physical chemistry, 98(12), 1994, pp. 3161-3164
Interactions of DNA bases represent a crucial source of DNA conformati
onal variability. Oligonucleotide crystal studies revealed a number of
base-base interactions which seem to be stabilized by nonplanar DNA b
ase amino groups. Therefore, an accurate description of the geometry a
nd deformability of the DNA base amino groups is very important. Here,
the second-order Moller-Plesset (MP2) 6-31G-optimized nonplanar geom
etries of adenine, cytosine, guanine, thymine, and isocytosine are pre
sented. The amino groups of the bases exhibit significant Sp3 pyramida
lization. The dihedral angles between the cytosine and adenine rings a
nd their amino group hydrogen atoms range from 10 to 25-degrees, and t
he nonplanar cytosine and adenine are 0.4 kcal/mol more stable than th
e planar molecules. Dihedral angles between the two guanine amino grou
p hydrogen atoms and the guanine ring are 43 and 12-degrees, and the n
onplanar guanine is 1.6 kcal/mol more stable than the planar molecule.
Isocytosine exhibits amino group properties similar to those of guani
ne. Selected DNA bases were also optimized using larger basis sets of
atomic orbitals: 6-31G*, DZP+, and DZ(2d). The MP2/6-31G** calculatio
ns yield results very similar to those of the MP2/6-31G calculations,
while the larger DZP+ and DZ(2d) basis sets indicate an even greater
amino group nonplanarity.