Precision neutron diffraction structure determination of protein and nucleic acid components. XII. A study of hydrogen bonding in the purine-pyrimidine base pair 9-methyladenine · 1-methylthymine

A neutron diffraction study of the 1 : 1 complex between 9-methyladenine and 1-methylthymine, C6H7N5· C6H8N2O2, has been carried out. The structure is monoclinic, space group P21/m, with two base pairs per unit cell; cell parameters a =8.304(2), b =6.552(2), c =12.837(3)Å, and β=106.83(5)°. The structure has been refined by full-matrix least squares techniques starting from the x-ray results of Hoogsteen [K. Hoogsteen, Acta Crystallogr. 12, 822 (1959); Acta Crystallogr. 16, 907 (1963)]. All hydrogen atoms have been located with a precision better than 0.01 Å, with the exception of methyl group hydrogens. The thymine molecules appear to be slightly disordered by means of a 180° rotation about N3 ··· C6, which has the effect of interchanging N1 and C5 while leaving the positions of all other atoms approximately unchanged. Between 10% and 13% of the thymine molecules in the structure are disordered in this way. Average refined neutron scattering lengths for nitrogen and carbon are b̄N=0.910(3) and b̄C=0.657(3) × 10−12 cm; oxygen and hydrogen scattering lengths were fixed at bH=−0.372 and b0=0.575 × 10−12 cm. The purine and pyrimidine bases are joined with N3 of thymine hydrogen bonded to N7 of adenine. Because of the disorder present in the structure, 87%–90% of the adenine · thymine pairs have the Hoogsteen configuration and the remainder have the reversed Hoogsteen configuration. These geometries differ from that of a Watson-Crick adenine · thymine pair in which N3 of thymine donates a proton to N1 of adenine. The hydrogen bonding scheme in the crystalline complex consists of one N–H ··· N and two N–H ··· 0 bonds and is quite normal; there is no evidence for proton transfer in any of the hydrogen bonds which are formed.