Stability of the 6-Carbanion of Uracil Analogues:  Mechanistic Implications for Model Reactions of Orotidine-5‘-monophosphate Decarboxylase

Abstract

The pK a 's of the 6-CH groups of N-methyl-2-pyridone and N-methyl-4-pyridone in aqueous solution were determined. No correlation between the stability of the carbanions and the rate of decarboxylation of corresponding carboxylic acids was found.The decarboxylation of 1,3-dimethylorotic acid (1) and its analogues has been proven to be a useful model for the enzymatic decarboxylation catalyzed by orotidine-5'-monophosphate decarboxylase (ODCase). [1][2][3][4][5][6][7][8][9][10][11][12] Most of the studies involve the investigation of the nature and stability of the intermediate. As shown in Scheme 1, acid 1 decarboxylates at elevated temperatures to give 1,3-dimethyluracil (2) as the sole product.The decarboxylation of acids 1, 4 and 5 to uracil 2 and pyridones 6 and 7 (Figure 1), respectively, provides a unique opportunity to systematically investigate the mechanism of the reactions due to the large difference in their reaction rates despite their structural similarity. 1,6,7 Acids 1 and 4 decarboxylate at the same rate, while acid 5 decarboxylates almost 3000 times faster. 1,7 Studies on the gas-phase stability of the corresponding carbanions 3, 8, and 9 have established a lack of correlation between the rate of decarboxylation and the gas-phase stability of resulted carbanions. 7 It was found that carbanion 3 is much more stable while carbanions 8 and 9 share the same stability. 6,7 As a result, a two-step mechanism has been proposed to account for the large difference in rate constants measured for acids 1, 4, and 5 (Scheme 2). 1,7 In this mechanism, the large differences in the equilibrium constants explain the differences in rate constants.The pK a of uracil 2 in water has been determined to be 34 ± 2, which is suggested to be the evidence for the high reaction barrier for catalysis by ODCase. 8 However, our gas-phase study has demonstrated that the stability of the carbanionic intermediates does not correlate with the rate of decarboxylation. 7 One concern about gas-phase studies is that the results may not represent those in condensed phase. In condensed phase, solvation plays a major rule in the wuw@sfsu.edu. relative stability of species, especially ions. In this report, we have extended the study on the stability of carbanions 3, 8, and 9 to the aqueous solution. NIH Public AccessAuthor Manuscript Org Lett. Author manuscript; available in PMC 2009 September 14.Richard and coworkers have determined pK a of weak carbon acids in aqueous solution by measuring the rate of proton-deuterium exchange on interested carbons using NMR spectroscopy. 13,14 This method was employed by Sievers and Wolfenden in determining the pK a of 6-CH of uracil 2. 8 However, when pyridones 6 and 7 were heated in acetate buffer in D 2 O as reported for 2, no proton-deuterium exchange was observed after 5 hrs. This observation indicates that pyridones 6 and 7 are less acidic than uracil 2 at carbon-6 and a much stronger base is required. Proton-deuterium exchange on carbon-6 of pyridones 6 and 7 has been reported in NaOD/D ...

Carbanions from decarboxylation of orotate analogs: Stability and mechanistic implications

“…The identical pK a values of the 6-CH groups of pyridones 5 and 6 in water ( Table 1) have confirmed that the stability of carbanions 8 and 9 are similar in at least one condensed phase, following the same trend as in the gas phase [6,7,13]. This result has further demonstrated that there is a lack of correlation between the stability of the carbanion and the rate of the decarboxylation (see Table 1).…”

“…This result has further demonstrated that there is a lack of correlation between the stability of the carbanion and the rate of the decarboxylation (see Table 1). However, the values from two separate studies on uracil 4 do not agree with each other very well [12,13]. The two studies were carried out using the same kinetic method but under somewhat different conditions due to the chemical reactivity of 4 [13].…”

“…The pK a values of the 6-CH groups of compounds 4-6 in water were determined in order to estimate the stability of carbanions 7-9 in aqueous medium [12,13]. Unfortunately, the pK a values determined for uracil 4 in two separate studies were not consistent as shown in Table 1 [12,13]. In this study, we report the estimated pK a values determined in DMSO, a solvent with similar properties to that employed in kinetic measurement of the decarboxylation reactions, sulfolane.…”

Stabilities of uracil and pyridone-based carbanions: a systematic study in the gas phase and solution and implications for the mechanism of orotidine-5′-monophosphate decarboxylase

“…7,8,13,14 The gas phase study was carried out in a quadrupole ion trap mass spectrometer where the carbanions were generated via collision activated dissociation (CAD) of precursor carboxylate anions derived from acids 1 – 3 as the result of electrospray ionization. 7,8 The carbanions were allowed to react with a series of neutral carbon acids with varying strength as seen in Table 1.…”

“…13 The rate of exchange is determined by the stability of the carbanion intermediate. The more stable the carbanion intermediate, the faster the exchange reaction.…”