Pyrimidine Nucleosides in Solution

Proton magnetic resonance (PMR) spectra of 45 nucleoside and nucleotide derivatives of uracil, thymine, cytosine, 5‐methylcytosine, and other substituted pyrimidines in water or dimethyl sulfoxide solutions have been analysed in order to correlate structure variations with molecular conformations and to gain insight into the nature of intramolecular forces which are responsible for the ‘rigidity’ of the molecules. Irrespective of the structure of pyrimidine base and the absolute chemical shift values (δ) the C(6)‐H and, to a lesser degree, the C(5)‐H and C(5)‐CH 3 resonances are shifted downfield by very similar amounts (Δδ) in the regular nucleosides or in the presence of charged or polar C‐4′ substituents. In detail, the following conformation‐determining effects are seen. 1. Ribose vs 2‐deoxyribose substitution of a pyrimidine makes little difference for the chemical environment of base hydrogens but an intact pentofuranose ring (4′‐O) and the exocyclic 5′‐OH group are essential for a nucleoside to assume a specific conformation. 2. Profound shielding or deshielding of H‐6 by exocyclic nitrate, halogen, hydroxyl, phosphate, and carboxylate substituents indicates preference for the anti and gauche, gauche conformation ranges in all compounds except in the case of C‐6 substitution. 3. Halogen atoms and the hydroxyl group (Δδ∼ 0.30–0.40 ppm) interact with pyrimidine bases by induced polarisation of the C(5)=C(6) double bond, phosphate anions (Δδ∼ 0.50 ppm) interact by the electrostatic attraction mechanism previously described, and in nucleoside 5′‐carboxylates (Δδ > 0.90 ppm) a hydrogen bond between −COO − and H‐6 is formed. 4. The deshielding effects caused by a 5′‐OH group and monoanionic 5′‐phosphate are similar (Δδ∼ 0.35–0.45 ppm), supporting the view that intramolecular rigidity of nucleosides and the nucleotide unit is not fundamentally different. This systematic survey, together with our previous studies of adenosine derivatives, provides a rationale for why the majority of both pyrimidine and purine nucleosides and nucleotides in solution exhibit closely comparable conformations, which in turn explain the group specificity of certain key enzymes in nucleic acid metabolism.