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S. Huang et al. / Tetrahedron Letters 52 (2011) 3960–3962
pyridinium compounds has a large impact on the reactivity. Com-
parison of pyridinium 5 and uracil 13 reveals rate acceleration of
more than 20,000-fold, although comparison of the rate constants
measured for 4 and 12 shows a much smaller effect. Methoxy sub-
stitution at the o-position, however, can contribute electron den-
sity to the pyridinium ring through resonance and thus reduce
the extent of rate enhancement. 6-Methoxypyridinium 10 is thus
sixfold less reactive than pyridinium 4. The iodo compound is less
reactive than the chloro compound presumably due to a combina-
tion of its lower electronegativity and larger size. If the radical
mechanism (one of the mechanisms8 proposed for the enzymatic
reaction) were operating for the model reactions studied here,
the iodo substrate will be the more reactive. These results are con-
sistent with the ‘element effect’ observed in the nucleophilic aro-
matic substitution reactions of 2,4-dinitrobezene derivatives.14,15
The results have also suggested that the first step in the proposed
mechanism is likely the rate-determining step.
The results obtained are consistent with the idea that the
pyrimidine structure is polarized in the active site of ODCase,
although the outright formation of a zwitterionic intermediate16,17
is unlikely due to the lack of basic residues adjacent to O-2 and O-4
as revealed by crystallographic studies.18–21 Deuterium exchange
studies on UMP have demonstrated the existence of a stabilized
carbanion intermediate in the enzymatic reaction.5,22 It has been
proposed that a pre-organized polar environment at the active site
due to its charge distribution stabilizes the carbanionic intermedi-
ate through dipole interactions.3,23,24 It is conceivable such dipole
interactions may alter the electron density distribution on the ura-
cil moiety to facilitate the nucleophilic attack at carbon-6 in the
hydrolysis of cyanoUMP 7. The results suggest that this feature of
the active site of ODCase can also explain its unexpected ability
to catalyze the hydrolysis reaction of 6-cyanoUMP 7.
from the Center for Computing for Life Sciences at SFSU. The NMR
facility was funded by the National Science Foundation (DUE-
9451624 and DBI 0521342). S.H. was supported by the Summer
Research Fellowship from the Department of Chemistry and Bio-
chemistry. In addition, we are indebted to Professor James Keeffe
at SFSU for helpful discussions.
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This investigation was supported by the National Institutes of
Health, MBRS SCORE Program—Grant S06 GM52588 and by a grant