ANHARMONIC AND HARMONIC INTERMOLECULAR VIBRATIONAL-MODES OF THE DNA-BASE PAIRS

Intermolecular vibrational modes of the H-bonded adenine...thymine Wat son-Crick (AT) base pair were studied for the first time using multidi mensional nonharmonic treatment. Relying on a Born-Oppenheimer-like se paration of the fast and slow vibrational motions, the complete multid imensional vibrational problem is reduced to a six-dimensional subprob lem in which all rearrangements between the pair fragments (i.e., aden ine and thymine) can be described. Following the Hougen-Bunker-Johns a pproach and using appropriate vibrational coordinates, a nonrigid refe rence is defined which covers all motions on the low-lying part of the intermolecular potential surface and which facilitates the derivation of a suitable model Hamiltonian. The potential energy surface is dete rmined at the ab initio Hartree-Fock level with minimal basis set (HF/ MINI-1) and an analytic potential energy function is obtained by fitti ng to the ab initio data. This function is used to calculate vibration al energy levels and effective geometries within the framework of the model Hamiltonian, disregarding the role of the kinematic and potentia l (in-plane)-(out-of-plane) interactions. The calculations are in reas onable agreement with the normal coordinate analysis (harmonic treatme nt) thus indicating physical correctness of this standard approach for an approximate description of the lowest vibrational states of the AT base pair. In addition, to get a deeper insight, harmonic vibrational frequencies of the AT pair and 28 other base pairs are evaluated at t he same and higher levels of theory [ab initio Hartree-Fock level with split-valence basis set (HF/6-31G*)]. The HF/MINI-1 and HF/6-31G** i ntermolecular harmonic vibrational frequencies differ by less than 30% . For all the base pairs, the buckle and propeller vibrational modes [ for definition and nomenclature see R. E. Dickerson et al., EMBO J. 8, 1 (1989)] are the lowest ones, all being in the narrow interval (from 4 to 30 cm(-1) in the harmonic approximation). Although most of the e valuated harmonic frequencies are qualitatively correct approximations to the genuine vibrational frequencies, in some cases due to a strong nonharmonic behavior of the buckle motion, they become physically mea ningless. To get physically correct results in such cases, apparently, the standard harmonic oscillator approach should be replaced by a mor e adequate approach, for instance, by the approach we used in the case of the adenine...thymine pair. (C) 1997 American Institute of Physics .