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

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.     

The acidity and proton affinity of the damaged base 1,N6-ethenoadenine in the gas phase versus in solution: intrinsic reactivity and biological implications

1,N(6)-ethenoadenine (epsilonA) is a highly mutagenic lesion that is excised from human DNA by the enzyme alkyladenine DNA glycosylase (AAG). In an effort to understand the intrinsic properties of 1,N(6)-ethenoadenine, we examined its gas phase acidity and proton affinity using quantum mechanical calculations and mass spectrometric experimental methods. We measure two acidities for epsilonA: a more acidic site (DeltaH(acid) = 332 kcal mol(-1); DeltaG(acid) = 325 kcal mol(-1)) and a less acidic site (DeltaH(acid) = 367 kcal mol(-1); DeltaG(acid) = 360 kcal mol(-1)). We also find that the proton affinity of the most basic site of 1,N(6)-ethenoadenine is 232-233 kcal mol(-1) (GB = 224 kcal mol(-1)). These measurements, when compared to calculations, establish that, under our experimental conditions, we have only the canonical tautomer of 1,N(6)-ethenoadenine present. We also compare the gas phase acidic properties of epsilonA with that of the normal bases adenine and guanine and find that epsilonA is the most acidic. This supports the theory that AAG and other related enzymes may cleave damaged bases as anions. Furthermore, comparison of the gas phase and aqueous acidities indicates that the nonpolar environment of the enzyme enhances the acidity differences of epsilonA versus adenine and guanine.     

Theoretical and experimental studies of cationized uracil complexes in the gas phase

Cationized uracil clusters were generated in the gas phase by electrospray ionization (ESI). Mass spectrometry experiments showed that with particular experimental conditions, decameric uracil clusters are magic number clusters. MS/MS experiments demonstrated that the structure of these decameric uracil clusters depends substantially on the size and the charge of the cation. On the basis of the ab initio and density functional theory (DFT) quantum chemistry calculations, structures for these decameric clusters were proposed. These structures are in agreement with the experimental mass spectra of modified nucleobases. Theoretical calculations showed that complexes experimentally observed using ESI-MS techniques, are not naturally the most stable in the gas phase.     

Acidity and proton affinity of hypoxanthine in the gas phase versus in solution: intrinsic reactivity and biological implications

Hypoxanthine is a mutagenic purine base that most commonly arises from the oxidative deamination of adenine. Damaged bases such as hypoxanthine are associated with carcinogenesis and cell death. This inevitable damage is counteracted by glycosylase enzymes, which cleave damaged bases from DNA. Alkyladenine DNA glycosylase (AAG) is the enzyme responsible for excising hypoxanthine from DNA in humans. In an effort to understand the intrinsic properties of hypoxanthine, we examined the gas-phase acidity and proton affinity using quantum mechanical calculations and gas-phase mass spectrometric experimental methods. In this work, we establish that the most acidic site of hypoxanthine has a gas-phase acidity of 332 +/- 2 kcal mol-1, which is more acidic than hydrochloric acid. We also bracket a less acidic site of hypoxanthine at 368 +/- 3 kcal mol-1. We measure the proton affinity of the most basic site of hypoxanthine to be 222 +/- 3 kcal mol-1. DFT calculations of these values are consistent with the experimental data. We also use calculations to compare the acidic and basic properties of hypoxanthine with those of the normal bases adenine and guanine. We find that the N9-H of hypoxanthine is more acidic than that of adenine and guanine, pointing to a way that AAG could discriminate damaged bases from normal bases. We hypothesize that AAG may cleave certain damaged nucleobases as anions and that the active site may take advantage of a nonpolar environment to favor deprotonated hypoxanthine as a leaving group versus deprotonated adenine or guanine. We also show that an alternate mechanism involving preprotonation of hypoxanthine is energetically less attractive, because the proton affinity of hypoxanthine is less than that of adenine and guanine. Last, we compare the acidity in the gas phase versus that in solution and find that a nonpolar environment enhances the differences in acidity among hypoxanthine, adenine, and guanine.     

The gas phase acidity of oligofluorobenzenes and oligochlorobenzenes: about the additivity or non-additivity of substituent effects

The deprotonation energies of benzene, fluorobenzene, all di-, tri-, and tetrafluorobenzenes, pentafluorobenzene, chlorobenzene, all di-, tri-, and tetrachlorobenzenes, and pentachlorobenzene have been calculated at various levels of second-order Moller-Plesset and density functional theory. Taking the previously determined experimental data as a benchmark, good agreement was achieved in the chloro series even with moderate computational effort, whereas more extended basis sets have to be used to obtain meaningful numbers in the fluoro series. Apparently, most extensive electron correlation is required to avoid artifacts caused by the proximity of nonbonding lone pairs at the carbanionic center and at the fluorine atoms. When two or more fluorine substituents were introduced in the same aromatic ring, their individual effects (as defined by position-dependent acidity increments) proved to be perfectly additive in the entire series. In contrast, the acidifying effect of chloro substituents was found to level off when the number of such halogens increases. Additivity or non-additivity of element effects cannot be ascertained after having merely compared the acidity of mono- and disubstituted substrates, but only after having moved to higher degrees of substitution.     

Tautomerism of pyrimidines and purines in the gas phase and in low-temperature matrices,and some biological implications

Infrared spectra in the NH, OH, and C?O stretching regions are reviewed for various methylated and halogenated 2(4)-oxopyrimidines and uracils, as well as other nucleic acid derivatives, in the vapor phase and in low-temperature matrices. The 2-oxopyrimidines are predominantly in the enol form both in the vapor phase and in low-temperature matrices. By contrast, the 4-oxopyrimidines exhibit comparable populations of the keto and enol forms, with K_T ≈ 1–2, and a difference in chemical binding energy between the two forms in the gaseous phase of the order of 1–2 kcal/mol. The observed tautomeric equilibria in the gas phase point to the need for a drastic revision of interpretations of theoretical methods, and simultaneously provide the appropriate quantitative data necessary for testing the results of quantum mechanical calculations. In sharp contrast to other heterocyclic systems, several of the bases found in natural nucleic acids were found to exist predominantly in the keto or amino forms, as in the solution phase. In particular, uracils exist predominantly in the keto form. This has made possible, for this class of compounds, to evaluate the heats of sublimation and vaporization, and to relate these data to hydrogen bonding and stacking interactions in the condensed phases. Examples are presented of base analogs which do exhibit appreciable tautomerism in solution. Some biological implications of the foregoing are presented in relation to the types of heterocyclic bases found in natural nucleic acids, and to concepts of spontaneous and induced mutagenesis.     

The kinetic acidity of oligofluorobenzenes correlated with their gas phase deprotonation energies

The relative reactivities of fluorobenzene, all di-, tri-, and tetrafluorobenzenes and pentafluorobenzene toward sec-butyllithium have been assessed in tetrahydrofuran at -100 degrees C. At this temperature no subsequent transmetalation reactions take place but those compromise the outcome of the competition experiments if the latter are conducted at -75 degrees C. The rates determined at -100 degrees C reflect the basicity differences between the naked (oligo)fluorophenyl anions to the extent of 10 %.     

Intrinsic acidity of dimethylhalonium ions: evidence for hyperconjugation in dimethylhalonium ylides in the gas phase

The intrinsic acidity of dimethylhalonium ions has been determined, both by theoretical methods and by gas-phase reactions of the isolated ions with pyridine bases. The calculated geometry of the dimethylhalonium ions shows a bent structure with the C-X-C angle decreasing in the order Cl > Br > I. Thermochemical calculations for the reaction of the dimethylhalonium ions with pyridine, 2,6-dimethylpyridine, and 2,6-di-tert-butylpyridine indicate that proton transfer, with the formation of the dimethylhalonium ylide is endothermic, whereas methyl transfer, with formation of methylhalide, is exothermic. The endothermicities for proton transfer are, nevertheless, dependent on the steric hindrance of the base. The bulkier the bases, the less endothermic the proton-transfer reaction is. Experimental gas-phase reactions support the calculations, showing that methyl transfer is the major reaction of dimethylchloronium and dimethyliodonium with pyridine, whereas proton transfer, as well as single electron transfer, is observed for the bulkier bases. The calculations also indicate that acidity increases in the order chloronium > bromonium > iodonium. NBO calculations predict that hyperconjugation with the sigma carbon-halogen orbital plays a role in stabilizing the halonium ylide species in the gas phase.     

Interaction of Ca2+ with uracil and its thio derivatives in the gas phase

The structures and relative stabilities of the complexes formed by uracil and its sulfur derivatives, namely, 2-thio-, 4-thio, and 2,4-dithio-uracil when interacting with Ca(2+) in the gas phase have been analyzed by means of density functional theory (DFT) calculations carried out at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31+G(d,p) level. For uracil and 2,4-dithiouracil, where the two basic sites are the same, Ca(2+) attachment to the heteroatom at position 4 is preferred. However, for the systems where both types of basic centers, a carbonyl or a thiocarbonyl group, are present, Ca(2+)-oxygen association is favored. The most stable complexes correspond to structures with Ca(2+) bridging between the heteroatom at position 2 of the 4-enol (or the 4-enethiol) tautomer and the dehydrogenated ring nitrogen, N3. The enhanced stability of these enolic forms is two-fold, on the one hand Ca(2+) interacts with two basic sites and on the other triggers a significant aromatization of the ring. Besides, Ca(2+) association has a clear catalytic effect on the tautomerization processes which connect the oxo-thione forms with the enol-enethiol tautomers. Hence, although the enol-enethiol tautomers of uracil and its thio derivatives should not be observed in the gas phase, the corresponding Ca(2+) complexes are the most stable species and should be accessible, because the tautomerization barriers are smaller than the Ca(2+) binding energies.     

Structures and fragmentation of [Cu(uracil-H)(uracil)]+ in the gas phase

Complexes of copper (II) ions and uracil were studied using tandem mass spectrometry (Fourier transform ion cyclotron resonance, FTICR, mass spectrometry) including extensive isotopic labeling as well as theoretical calculations. Positive ion electrospray mass spectra of aqueous solutions of CuCl(2) and uracil show that the [Cu(Ura-H)(Ura)](+) ion is the most abundant ion even at low concentrations of uracil. Sustained off-resonance irradiation collision-induced dissociation (SORI-CID) experiments show that the lowest energy decomposition pathway for [Cu(Ura-H)(Ura)](+) , surprisingly, is not the loss of uracil, but the loss of HNCO followed by HCN as the most abundant secondary fragmentation product. MS(n) studies identified primary, secondary and tertiary fragmentation products. Extensive isotopic labeling studies, as well as computational studies allowed for a detailed fragmentation scheme for the [Cu(Ura-H)(Ura)](+) ion, beginning with the lowest energy structure.     

The acidity of chloro-substituted benzenes: a comparison of gas phase, ab initio, and kinetic data

The deprotonation energies of benzene, chlorobenzene, all di-, tri-, tetrachlorobenzenes, and pentachlorobenzene have been determined in the gas phase using a Fourier transform ion cyclotron resonance mass spectrometer. The values measured differ only slightly, though significantly, from the corresponding data for oligofluorobenzenes. The heavier halogen acidifies orthopositions slightly less and meta-positions slightly more than fluorine does. Moreover, the contributions of three or more chloro substituents are not perfectly additive. In fact the accumulation attenuates the contributions somewhat. Quantum chemical calculations at the MP2/6-311+G* level reproduce the gas-phase acidities fairly well, but reveal special effects when extended to experimentally not observable benzenides carrying the halogens at anion-remote positions. Competition experiments have been performed to assess the relative reactivity of nine oligochlorobenzenes towards sec-butyllithium in tetrahydrofuran at -100 degrees C. An almost exact linear correlation between logarithmic rates and gas-phase acidities has been found.     

Extremal acidity of Rees polycyanated hydrocarbons in the gas phase and DMSO--a density functional study

It is shown by using the density functional theory (DFT) calculations that Rees tricyclic[10]annulene 1 and its benzo-annelated derivative 2, substituted by CN groups at all peripheral sp2 carbon positions, represent hyperstrong neutral superacids in the gas-phase and DMSO.     

Absorption and fluorescence spectra of uracil in the gas phase and in aqueous solution: a TD-DFT quantum mechanical study

Here we present the first computations of fluorescence spectra in aqueous solution at an accurate quantum mechanical level. From a methodological point of view, our study shows that by only taking into account both bulk effects and explicit solvent molecules it is possible to reproduce solvent effects on the energy and the intensities of the electronic spectra, especially for what concerns pi/pi* transition. The computed absorption and fluorescence spectra are in a good agreement with the available experimental results. The energy ordering between the lowest energy n-pi* and the pi/pi* transitions in uracil strongly depends on the nature of the embedding medium. The geometry of the first solvation shell is remarkably sensitive to the specific electronic state, suggesting that solvent degrees of freedom can act as S1/S2 coupling modes.     

Comparative quantum-chemical investigation of the CH acidity of some N-methyl-amino derivatives in the gas phase and in solution

The equilibrium configuration of the molecules of three derivatives of N-methylnitrosoamine, N,N-dimethylnitramine, and 1-phenyl-1-triazene and their carbanions were calculated by various semiempircal SCF methods and also in the nonempirical 3–21G⁺ approximation. The optimized geometric parameters of the AM-1 method and the nonempirical 3–21G⁺ calculation agree with each other and with the experimental data better than the geometric parameters calculated by the MINDO/3 method. The most reliable results are obtained by the AM1 method as applied to the gasphase CH acidity of the N-methylamino derivatives. The scheme for the breakdown of the deprotonation energies of the investigated CH acids into components characterizing the individual atoms and bonds was used to analyze the mechanism of internal stabilization of the conjugated carbanions. Comparison of the kinetic CH acidities of the standard hydrocarbons in the basic solution with their deprotonation energies calculated by the AM1 method made it possible to obtain a correlation, the existence of which confirms that there is a single type of mechanism for the stabilization of the carbanions, excluding the solvation effect. The deviation of N-methylamino derivatives from the main line indicates that the solvent has a strong effect on their kinetic CH acidity.Scientific-Production Association, State Institute of Applied Chemistry, Leningrad. Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 27, No. 4, pp. 426–437, July–August, 1991. Original article submitted February 25, 1991.     

Effects of hydrogen-bonding and stacking interactions with amino acids on the acidity of uracil

The effects of hydrogen-bonding interactions with amino acids on the (N1) acidity of uracil are evaluated using (B3LYP) density functional theory. Many different binding arrangements of each amino acid to three uracil binding sites are considered. The effects on the uracil acidity are found to significantly depend upon the nature of the amino acid and the binding orientation, but weakly depend on the binding site. Our results reveal that in some instances small models for the amino acids can be used, while for other amino acids larger models are required to properly describe the binding to uracil. The gas-phase acidity of uracil is found to increase by up to approximately 60 kJ mol(-1) due to discrete hydrogen-bonding interactions. Although (MP2) stacking interactions with aromatic amino acids decrease the acidity of uracil, unexpected increases in the acidity are found when any of the aromatic amino acids, or the backbone, hydrogen bond to uracil. Consideration of enzymatic and aqueous environments leads to decreases in the effects of the amino acids on the acidity of uracil. However, we find that the magnitude of the decrease varies with the nature of the molecule bound, as well as the (gas-phase) binding orientations and strengths, and therefore solvation effects should be considered on a case-by-case basis in future work. Nevertheless, the effects of amino acid interactions within enzymatic environments are as much as approximately 35 kJ mol(-1). The present study has general implications for understanding the nature of active site amino acids in enzymes, such as DNA repair enzymes, that catalyze reactions involving anionic nucleobase intermediates.     

Selective molecular recognition of arginine by anionic salt bridge formation with bis-phosphate crown ethers: implications for gas phase peptide acidity from adduct dissociation

Arginine forms a stable noncovalent anionic salt bridge complex with DP (a crown ether which contains two endocyclic dialkylhydrogenphosphate esters). Abundant adduct formation with DP is observed for complexes with arginine, YAKR, HPPGFSPFR, AAKRKAA, RR, RPPGFSPFR, RYLGYL, RGDS, and YGGFMRGL in electrospray ionization mass spectrometry (ESI-MS) experiments. DFT calculations predict a hydrogen bonded salt bridge structure with a protonated guanidinium flanked by two deprotonated phosphates to be the lowest energy structure. Dissociation of DP/peptide adducts reveals that, in general, the relative gas phase acidity of a peptide is dependent on peptide length, with longer peptides being more acidic. In particular, peptides that are six residues or more in length can stabilize the deprotonated C-terminus by extensive hydrogen bonding with the peptide backbone. Dissociation of DP/peptide complexes often yields the deprotonated peptide, allowing for the facile formation of anionic peptides that otherwise would be difficult to generate in high abundance. Although DP has a preference for binding to arginine residues in peptides, DP is also observed to form less abundant complexes with peptides containing multiple lysines. Lys-Xxx-Lys and Lys-Lys sequences form low abundance anionic adducts with DP. For example, KKKK exclusively forms a double adduct with one net negative charge on the complex.     

Microsolvation of uracil and its conjugate bases: a DFT study of the role of solvation on acidity

The effect of microsolvation on the deprotonation energies of uracil was examined using DFT. The structures of uracil and its N(1) and N(3) conjugate bases were optimized with zero to six associated water molecules. Multiple configurations (upward of 93) of these hydrated clusters were located at PBE1PBE/6-311+G(d,p). Trends in these geometries are discussed, with the waters generally forming chains with small numbers of waters (one-three), rings (three-five waters), or cages (five-six waters). The difference in energy between the N1 and N3 conjugate bases is 13 kcal mol(-1) in the gas phase, and it decreases with each added water up to four. At this point the energy difference has been halved, but addition of a fifth or sixth water has little effect on the energy difference. This is understood in terms of the water structures and their ability to stabilize the negatively charged atoms in the conjugate bases.     

A gas phase ab initio excited state geometry optimization study of thymine, cytosine and uracil

Molecular geometries of the nucleic acid bases thymine, cytosine and uracil in the ground and the lowest two singlet excited states were optimized using the ab initio approach employing the 4-31G basis set for all the atoms except the amino group of cytosine for which the 6-311+G^* basis set was used. The excited state calculations were performed employing configuration interaction involving singly excited configurations (CIS). Vibrational frequencies were computed in order to examine the nature of the stationary points on the potential energy surfaces obtained by geometry optimization. While the ground state geometries of uracil and thymine (except the methyl group hydrogens) are planar, the corresponding excited state geometries were found to be significantly nonplanar. In the case of cytosine, the amino group is pyramidal and the rest of the molecule is only slightly nonplanar in the ground state, but the excited state geometries are appreciably nonplanar. In particular, consequent to the S₂(n–π^*) excitation of cytosine, the amino group plane is strongly rotated. While thymine is stable in the S₂(π–π^*) excited state, uracil appears to be dissociative in the corresponding excited state.