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The MP2/6-31G(d) structures of the pyrimidine nucleosides differ in the relative orientation of the base with respect to the nucleoside. For example, the ∠(O4′C1′N1C2) dihedral angle equals -153.7° in deoxycytidine, but equals -129.4° in deoxythymidine. This difference in rotation about the glycosidic bond implies that the amino acid is further away from the C2′ hydrogen atoms when stacked with thymine (or uracil) compared with cytosine
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