Intramolecular nondissociative proton transfer in aqueous solutions of tautomeric heterocycles: a temperature-jump kinetic study

Next-Generation Tags for Fluorine Nuclear Magnetic Resonance: Designing Amplification of Chemical Shift Sensitivity

Fluorine NMR is a highly sensitive technique for delineating the conformational states of biomolecules and has shown great utility in drug screening and in understanding protein function. Current fluorinated protein tags leverage the intrinsic chemical shift sensitivity of the 19F nucleus to detect subtle changes in protein conformation and topology. This chemical shift sensitivity can be amplified by embedding the fluorine or trifluoromethyl reporter within a pyridone. Due to their polarizability and rapid tautomerization, pyridones exhibit a greater range of electron delocalization and correspondingly greater 19F NMR chemical shift dispersion. To assess the chemical shift sensitivity of these tautomeric probes to the local environment, 19F NMR spectra of all possible monofluorinated and trifluoromethyl-tagged versions of 2-pyridone were recorded in methanol/water mixtures ranging from 100% methanol to 100% water. 4-Fluoro-2-pyridone and 6-(trifluoromethyl)-2-pyridone (6-TFP) displayed the greatest sensitivity of the monofluorinated and trifluoromethylated pyridones, exceeding that of known conventional CF3 reporters. To evaluate the utility of tautomeric pyridone tags for 19F NMR of biomolecules, the alpha subunit of the stimulatory G protein (Gsα) and human serum albumin (HSA) were each labeled with a thiol-reactive derivative of 6-TFP and the spectra were recorded as a function of various adjuvants and drugs. The tautomeric tag outperformed the conventional tag, 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide through the improved resolution of several functional states.

Role of tautomerism in RNA biochemistry

Heterocyclic nucleic acid bases and their analogs can adopt multiple tautomeric forms due to the presence of multiple solvent-exchangeable protons. In DNA, spontaneous formation of minor tautomers has been speculated to contribute to mutagenic mispairings during DNA replication, whereas in RNA, minor tautomeric forms have been proposed to enhance the structural and functional diversity of RNA enzymes and aptamers. This review summarizes the role of tautomerism in RNA biochemistry, specifically focusing on the role of tautomerism in catalysis of small self-cleaving ribozymes and recognition of ligand analogs by riboswitches. Considering that the presence of multiple tautomers of nucleic acid bases is a rare occurrence, and that tautomers typically interconvert on a fast time scale, methods for studying rapid tautomerism in the context of nucleic acids under biologically relevant aqueous conditions are also discussed.

Direct observation of ground-state lactam-lactim tautomerization using temperature-jump transient 2D IR spectroscopy

We provide a systematic characterization of the nanosecond ground-state lactam-lactim tautomerization of pyridone derivatives in aqueous solution under ambient conditions using temperature-jump transient 2D IR spectroscopy. Although electronic excited-state tautomerization has been widely studied, experimental work on the ground electronic state, most relevant to chemistry and biology, is lacking. Using 2D IR spectroscopy, lactam and lactim tautomers of 6-chloro-2-pyridone and 2-chloro-4-pyridone are unambiguously identified by their unique cross-peak patterns. Monitoring the correlated exponential relaxation of these signals in response to a laser temperature jump provides a direct measurement of the nanosecond tautomerization kinetics. By studying the temperature, concentration, solvent, and pH dependence, we extract a thermodynamic and kinetic characterization and conclude that the tautomerization proceeds through a two-state concerted mechanism. We find that the intramolecular proton transfer is mediated by bridging water molecules and the reaction barrier is dictated by the release of a proton from pyridone, as would be expected for an efficient Grothuss-type proton transfer mechanism.

Theoretical studies of proton-transfer reactions of 2-hydroxypyridine--(H2O)n (n = 0-2) in the ground and excited states

The potential energy profiles for proton-transfer reactions of 2-hydroxypyridine and its complexes with water were determined by MP2, CASSCF and MR-CI calculations with the 6-31G** basis set. The tautomerization reaction between 2-hydroxypyridine (2HP) and 2-pyridone (2PY) does not take place at room temperature because of a barrier of approximately 35 kcal/mol for the ground-state pathway. The water-catalyzed enol-keto tautomerization reactions in the ground state proceed easily through the concerted proton transfer, especially for the two-water complex. The S1 tautomerization between the 2HP and 2PY monomers has a barrier of 18.4 kcal/mol, which is reduced to 5.6 kcal/mol for the one-water complex and 6.4 kcal/mol for the two-water complex. The results reported here predict that the photoinduced tautomerization reaction between the enol and keto forms involves a cyclic transition state having one or two water molecules as a bridge.

Reaction paths of tautomerization between hydroxypyridines and pyridones

Tautomerization paths of 2(and 4)-hydroxypyridine (called here HP) to 2(and 4)-pyridone (called here PY) with water molecules were investigated by the use of density functional theory calculations. Potential energies were compared for a number of water molecules. The 2-HP molecule was found to be isomerized most readily and concertedly to the 2-PY one via proton relays with two water molecules. The reaction pattern is invariant even when outer water molecules are added. The 4-HP(H(2)O)(n) --> 4-PY(H(2)O)(n) reaction model did not give small activation energies. However, a reaction of (4-HP)(2)(H(2)O)(2) --> (4-PY)(2)(H(2)O)(2) was found to occur readily through a transient ion-pair intermediate. The conversion processes of (2-PY)(2) to the tautomerization reacting system were discussed. The hydrogen-bond directionality regulates the tautomerization paths.

Q-mode curve resolution of UV–vis spectra for structural transformation studies of anthocyanins in acidic solutions

Chemometric analysis of ultraviolet-visible (UV-vis) spectra for pH values 1.0, 3.3, 5.3, and 6.9 was used to investigate the kinetics and the structural transformations of anthocyanins in extracts of calyces of hibiscus flowers of the Hibiscus acetosella Welw. ex Finicius for the first time. Six different species were detected: the quinoidal base (A), the flavylium cation (AH+), the pseudobase or carbinol pseudobase (B), cis-chalcone (C(C)), trans-chalcone (C(t)), and ionized cis-chalcone (C(C)-). Four equilibrium constant values were calculated using relative concentrations, hydration, pK(h) = 2.60 +/- 0.01, tautomeric, K(T) = 0.14 +/- 0.01, acid-base, pK(a) = 4.24 +/- 0.04, and ionization of the cis-chalcone, pK(C(C)) = 8.74 +/- 1.5 x 10(-2). The calculated protonation rate of the tautomers is K(H+) = 0.08 +/- 7.6 x 10(-3). These constants are in excellent agreement with those measured previously in salt form. From a kinetic viewpoint, the situation encountered is interesting since the reported investigation is limited to visible light absorption in acid medium. These models have not been reported in the literature.

Two competitive routes in the lactim-lactam phototautomerization of a hydroxypyridine derivative cation in water: dissociative mechanism versus water-assisted proton transfer

Ground-state tautomerism and excited-state proton-transfer processes of 2-(6'-hydroxy-2'-pyridyl)benzimidazolium in H2O and D2O have been studied by means of UV-vis absorption and fluorescence spectroscopy in both steady-state and time-resolved modes. In the ground state, this compound shows a tautomeric equilibrium between the lactim cation, protonated at the benzimidazole N3, and its lactam tautomer, obtained by proton translocation from the hydroxyl group to the pyridine nitrogen. Direct excitation of the lactam tautomer leads to its own fluorescence emission, while as a result of the increase of acidity of the OH group and basicity at the pyridine N upon excitation, the lactim species undergoes a proton translocation from the hydroxyl group to the nitrogen, favoring the lactam structure in the excited state. No fluorescence emission from the initially excited lactim species was detected due to the ultrafast rate of the excited-state proton-transfer processes. The lactim-lactam phototaumerization process takes place via two competitive excited-state proton-transfer routes: a one-step water-assisted proton translocation (probably a double proton transfer) and a two-step pathway which involves first the dissociation of the lactim cation to form an emissive intermediate zwitterionic species and then the acid-catalyzed protonation at the pyridine nitrogen to give rise to the lactam tautomer.

Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue

The hairpin ribozyme is a small catalytic RNA with reversible phosphodiester cleavage activity. Biochemical and structural studies exclude a requirement for divalent metal cation cofactors and implicate one active site nucleobase in particular, G8, in the catalytic mechanism. Our previous work demonstrated that the cleavage activity that is lost when G8 is replaced by an abasic residue is restored when certain nucleobases are provided in solution. The specificity and pH dependence of exogenous nucleobase rescue were consistent with several models of the rescue mechanism, including general acid base catalysis, electrostatic stabilization of negative charge in the transition state or a requirement for protonation to facilitate exogenous nucleobase binding. Detailed analyses of exogenous nucleobase rescue for both cleavage and ligation reactions now allow us to refine models of the rescue mechanism. Activity increased with increasing pH for both unmodified ribozyme reactions and unrescued reactions of abasic variants lacking G8. This similarity in pH dependence argues against a role for G8 as a general base catalyst, because G8 deprotonation could not be responsible for the pH-dependent transition in the abasic variant. Exogenous nucleobase rescue of both cleavage and ligation activity increased with decreasing pH, arguing against a role for rescuing nucleobases in general acid catalysis, because a nucleobase that contributes general acid catalysis in the cleavage pathway should provide general base catalysis in ligation. Analysis of the concentration dependence of cytosine rescue at high and low pH demonstrated that protonation promotes catalysis within the nucleobase-bound ribozyme complex but does not stabilize nucleobase binding in the ground state. These results support an electrostatic stabilization mechanism in which exogenous nucleobase binding counters negative charge that develops in the transition state.

Infrared studies of tautomerism in 2-hydroxypyridine 2-thiopyridine and 2-aminopyridine

The infrared spectra of 2-hydroxypyridine (2-OHP), 2-thiopyridine (2-SHP), and 2-aminopyridine (2-NH2P) have been recorded in the solid, liquid and vapor phases in the region 4000-200 cm(-1). To support the work, deuterated forms of these compounds in the functional groups XH and NH with (X=O, S, NH) were recorded for the solid and liquid phases. The results show existence of each compound as an equilibrium mixture of two tautomers in monomeric and cyclic dimeric forms in the solid, liquid and vapor phases. The monomers are predominant in the vapor phase. Enthalpy differences between the monomeric tautomers and activation energies for their inter-conversion were determined in each phase.