Molecular orbital calculations on the conformation of nucleic acids and their constituents: I. Conformational energies of β-nucleosides with C(3′)- and C(2′)-endo sugars

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Molecular orbital calculations, using the all-valence-electrons PCILO method, are carried out for the evaluation of conformational energies of purine and pyrimidine nucleosides as a function of the rotation about the C-N glycosidic linkage. In distinction to previous empirical treatments which were based on the partitioning of the potential energy into different constituents and a separate evaluation of those, the quantum-mechanical computations provide directly the total molecular energy corresponding to the different geometrical arrangements of the atoms. Explicit distinction is also made in the calculations for cases in which an intramolecular hydrogen bond is or is not formed between the sugar and base. Evaluation of the conformation energies is completed by evaluation of the relative probabilities of finding the nucleosides in the anti or syn regions. Results are presented for purine and pyrimidine glycosides with C(3′)-endo and C(2′)-endo sugars and compared with the available experimental data from X-ray studies on crystals.