Trans-hydrogen-bond (h2)J(NN) and (h1)J(NH) couplings in the DNA A-T base pair: natural bond orbital analysis.

Abstract

Natural bond orbital (NBO) analysis described here demonstrates that trans-hydrogen-bond (trans-H-bond) NMR J couplings in the DNA A-T base pair, h2JNN and h1JNH, are determined largely by three terms: two Lewis-type contributions (the single-orbital contribution from the adenine lone pair and the contribution from the sigmaN3H3 natural bond orbital of the thymine ring) and one contribution from pairwise delocalization of spin density (between the lone pair in adenine and the sigma* antibonding orbital linking N3 and H3 of thymine). For h2JNN coupling, all three contributions are positive, whereas for h1JNH coupling, the delocalization term is negative, and the other two terms are positive, resulting in a small net positive coupling constant. This result rationalizes the experimental findings that the two-bond coupling (h2JNN approximately 9 Hz) is larger than the one-bond coupling (h1JNH approximately 3 Hz) and demonstrates that the same hyperconjugative and steric mechanisms that stabilize the H-bond are involved in the transmission of J coupling information. The N1...H3-N3 H-bond of the DNA A-T base pair is found to exhibit significant covalent character, but steric effects contribute almost equally to the trans-H-bond coupling.