Figure 3.

Molecular orbital calculations. Ab initio geometries were calculated with the program SPARTAN (Wave-function, Irvine, CA) as described.³⁷ 1-Methylcytosine (instead of the sugar ring at position 1) was used to model the flipped base. Dark blue indicates a high value for the orbital, and the red indicates a low value, while green/yellow is in between. High values for the lowest unoccupied molecular orbital (LUMO) are seen over C6 and C4 for both 1-methylcytosine and N3 protonated 1-methylcytosine in all three cases, indicating that these are potential sites for nucleophilic attack. The 1-methyl-6-sulfhydryl-enol derivative of cytosine was used to model the intermediate formed by the enzyme after nucleophilic attack at C6. High values of the highest occupied molecular orbital (HOMO) are confined to C5 in cytosine and FdC, where the highly reactive orbital at C5 is then poised for attack on the methyl group of AdoMet, but between C4 and C5 in 2-H pyrimidinone. This is consistent with the observation that zebularine does not seem to be methylated at all.³⁸