The gas phase proton affinity of uracil: measuring multiple basic sites and implications for the enzyme mechanism of orotidine 5′-monophosphate decarboxylase

Abstract

We have shown for the first time experimentally that the O2 and O4 sites of uracil have different proton affinities, and as implied in previous computational studies, the O4 is more basic and would be energetically preferred in an orotate ribose 5'-monophosphate decarboxylase catalysis mechanism involving proton transfer to oxygen.

Infrared multiple photon dissociation action spectroscopy of protonated uracil and thiouracils: Effects of thioketo-substitution on gas-phase conformation

“…The activation barriers to form other tautomers of uracil are sufficiently high that these conformers are unlikely to be populated. Several experimental studies [25][26][27] have sought to determine the proton affinity of uracil, and with the aid of theoretical studies [28][29][30][31], to characterize its gas-phase structure. However, the structural information determined using high-pressure mass spectrometry (HPMS) and Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry experiments along with theoretical calculations are generally ambiguous.…”

Unimolecular Reactivity of Uracil–Cu2+ Complexes in the Gas Phase

“…For this reason much effort has been devoted to investigating the reactivity of this compound and its acidity, [1][2][3][4][5][6] basicity, [2,7] hydrogen-bonding ability towards other DNA species, [2] and solvation by water molecules. [2,4,5,8] Interaction with metal ions is also an important part of this research activity, [9][10][11][12][13] due to its ubiquitous presence in biological media, where it participates in different processes, such as enzyme regulation and stabilization of nucleic acids.…”

Gas-phase interactions between lead(II) ions and thiouracil nucleobases: A combined experimental and theoretical study

“…We have considered monodentate coordination either on X or Y heteroatom (C(2) or C(4) carbonyl or thiocarbonyl, respectively) (see Figure 1S of the supplemental information, which can be found in the electronic version of this article). Dissociation energies D 0 , calculated at 0 K are gathered in the Table 2 together with experimental proton affinities [9,40]. Note that the D 0 values were estimated without considering BSSEs, which are negligible at this level of theory [23].…”