Quantum chemical studies on the conformational structure of nucleic acids IV. calculation of backbone structure by CNDO method

Abstract

Quantum chemical calculations using the CNDO/2 method, have been carried out to determine the energetically favoured ranges of the torsional angles (φ',ω',ω,φ,ψ) which fix the conformational structure of nucleic acid backbone. The two dimensional isoenergy maps have been constructed in the (ω',ω) and (φ,ψ) hyperspaces. The variation of total energy with respect to φ' has also been studied. The results show that the non-bonding interactions play a major role in the conformational stability of nucleic acids and polynucleotides. The theoretical predictions show good correspondence with the experimental data (X-ray and ¹³C NMR) as well as the other reported theoretical calculations (EHT, PCILO and classical potential functions). The most favoured structure has the conformational angles close to 240, 290, 290, 180 and 60° and these values lead to a helical structure with a pitch of 34 Å and about ten nucleotide units per turn of the helix. The proposed models of Watson & Crick, DNA-B and DNA-C lie in high energy regions.