A quantum-dynamics study of the prototropic tautomerism of guanine and its contribution to spontaneous point mutations in Escherichia coli

High-level quantum-chemical and quantum-dynamics calculations are reported on the tautomerization equilibrium and rate constants of guanine and its complexes with one and two water molecules. The results are used to estimate the fraction of guanine present in the cell during DNA synthesis as the unwanted tautomer that forms an irregular base pair with thymine, thus giving rise to a spontaneous GC --> AT point mutation. A comparison of the estimated mutation frequency with the observed frequency in Escherichia coli is used to analyze two proposed mechanisms, differing in the extent of equilibration reached in the tautomerization reaction. In the absence of water, the equilibrium concentration of tautomeric forms is relatively large, but the barrier to their formation is high. If water is present, tautomeric forms are less favored, but water molecules may serve as efficient proton conduits causing rapid tautomerization. It is tentatively concluded that the mechanism in which a high tautomerization barrier keeps the tautomeric transformation far from a state of equilibrium is more likely than a mechanism in which water and/or polymerases produce a low equilibrium concentration of the tautomeric forms.     

Study of the Tautomerism by Experimentally and Theoretically Estimated 13C and 15N Chemical Shifts

2-Substituted 5-Me-7OH-1,2,4-Triazolo[1,5-a]pyrimidines can exist as different tautomeric forms. The tautomeric equilibrium of these compounds were determined by various NMR spectroscopic methods and quantum-chemical calculations. The tautomeric equilibria of 2-substituted 1,2,4-Triazolopyrimidines depend on the used solvent. In order to take solvent effects into account, ab initio calculations using the SCI-PCM method were carried out. The solvation energy depends on the polarity of the substituents in position 2. The comparison of chemical shifts determined by experimental methods and theoretical ab initio methods were used to definitely find out the the tautomeric equilibria of these compounds.     

Consequences of one-electron oxidation and one-electron reduction for 4-aminopyrimidine—DFT studies

The consequences of one-electron oxidation and one-electron reduction were studied for 4-aminopyrimidine (4APM), which displays prototropic tautomerism. Since experimental techniques are incapable of detecting less than 0.1% of minor tautomers, quantum-chemical calculations [DFT(B3LYP)/6-311+G(d,p)] were carried out for all possible tautomers of neutral 4AMP and its redox forms, 4APM (+ ?) and 4APM (- ?). Four tautomers were considered: one amine and three imine tautomers (two NH and one CH form). Geometric isomerism of the exo?=?NH group was also taken into account. One-electron oxidation (4APM - e → 4APM (+??)) has no significant effect on the tautomeric preferences; it influences solely the composition of the tautomeric mixture. The amine tautomer is favored for both 4APM (+??) and 4APM. An interesting change in the tautomeric preference occurs for 4APM (- ?). One-electron reduction (4APM?+?e → 4APM (- ?)) favors the C5 atom for the labile proton. The preference of the imine CH tautomer in the tautomeric mixture of 4APM (- ?) may partially explain the origin of CH tautomers in nucleobases.     

Structure and tautomerism of the neutral and monoanionic forms of 2-thiouracil, 2,4-dithiouracil, their nucleosides, and some related derivatives

Ultraviolet and infrared spectrophotometric techniques have been utilized to demonstrate that the monoanionic form of 2-thiouracil in aqueous medium consists of an equilibrium mixture of two tautomeric monoanions, one due to dissociation of the N1 proton, the other to dissociation of the N3 proton, in the approximate ratio 1:1. In contrast to 2,4-diketopyrimidines, and 4-thiouracil, where monoanion formation involves charge delocalization, the two tautomeric monoanions of 2-thiouracil appear to have the charge localized on the O4 position. The neutral forms of 2,4-dithiouracil and 2,4-dithiouridine are in the dithione form in both aqueous and non-aqueous media. The monoanionic form of 2,4-dithiouracil consists of a mixture of two tautomeric monoanions, the predominant one of which is that with the proton on the ring N3, and with charge delocalization on both isomeric monoanions. Such charge delocalization is also present in the monoanion of 2,4-dithiouridine. For the reference compound 2-methylthiopyrimidone-4, the dominant, virtually exclusive, form in chloroform is that with the hydrogen localized on the ring N3, whereas in aqueous medium there is a 1:1 equilibrium mixture of two neutral tautomeric forms, one with the hydrogen on N3, the other with the hydrogen on N1.     

Investigation of tautomeric composition of cytosine by multiphoton excitation spectra. II. Two-photon absorption spectra

For the first time the quantum-mechanical calculations of intensity distribution in the two-photon absorption spectra of the six tautomeric forms of cytosine were performed. It has been confirmed that in the aqueous solution of cytosine (pH 3.0) there exist several tauromeric forms: canonical amino-oxo tautomeric form, cation, as well as cys-imino-oxo and cys-amino-hydroxy tautomers.     

DFT studies on one-electron oxidation and one-electron reduction for 2- and 4-aminopyridines

Quantum-chemical calculations {DFT(B3LYP)/6-311+G(d,p)} were performed for all possible tautomers (aromatic and nonaromatic) of neutral 2- and 4-aminopyridines and their oxidized and reduced forms. One-electron oxidation has no important effect on the tautomeric preference for 2-aminopyridine. The amine tautomer is favored. However, oxidation increases the stability of the imine NH tautomer, and its contribution in the tautomeric mixture cannot be neglected. In the case of 4-aminopyridine, one-electron oxidation increases the stability of both the amine and imine NH tautomers. Consequently, they possess very close energies. As major tautomers, they dictate the composition of the tautomeric mixture. The CH tautomers may be considered as very rare forms for both neutral and oxidized aminopyridines. A reverse situation takes place for the reduced forms of aminopyridines. One-electron reduction favors the C3 atom for the labile proton for both aminopyridines. This may partially explain the origin of the CH tautomers for the anionic states of nucleobases containing the exo NH(2) group.     

Helix-forming conformers in structural organization of methylamides of N-acetyl-alpha-L-amino acids. Quantum-chemical study

Based on the results of quantum-chemical PM3 calculations, some common structural and thermodynamic properties of low-energy monopeptide conformers have been revealed that may be responsible for the initiation of alpha- or beta-like forms in polypeptide structures.     

Misincorporation of 2'-deoxyoxanosine into DNA: a molecular basis for NO-induced mutagenesis derived from theoretical calculations

A wide range of theoretical methods, including high level ab initio, density functional, self-consistent reaction field, molecular dynamics and thermodynamic integration calculations, have been used to analyze the mutagenic properties of oxanosine. The major tautomeric forms in the gas phase and aqueous solution have been determined. The ability of oxanosine to recognize thymine and cytosine in the gas phase and in the DNA environment has been compared with that of guanine. A physicochemical explanation for the mutagenic properties of oxanosine is suggested.     

Recognition modes of hypoxanthine,xanthine and their derivatives by amino acid carboxylic group: UV spectroscopic and quantum chemical data

UV absorption spectra of Hyp, Xan, their nucleosides and methyl derivatives were studied in anhydrous dimethylsuloxide and the changes in these spectra on the interactions with neutral and deprotonated carboxylic groups of amino acids were traced. By the semiempirical quantum-chemical method MNDO/H it was shown, that interaction with carboxylate-ion fixes Hyp as the rare N7H enolic tautomer and converts Xan into its N9H diketo tautomeric form with a probable admixture of the N7H O6-enolic form. Significant changes in the UV spectra of Xan, m3Xan, m9Xan and X under interaction with carboxylate-ion are determined by essential contribution to complex formation of proton transfer from bases to ligands, m9Xan and X proving to be slightly protonated even by the solvent. The methylation of the N7 position in m7I and m7X was established to result in the practical absence of their interactions with carboxylate-ion and initiation of a new ability of forming complex with the neutral carboxylic group. Substitution of the C8H group by N in 8-azaXan does not change the interaction specificity of the base with two forms of carboxylic group.     

Anticancer, neuroprotective activities and computational studies of 2-amino-1,3,4-thiadiazole based compound

Anticancer activity studies of 2-(4-fluorophenylamino)-5-(2,4-dihydroxyphenyl)-1,3,4-thiadiazole (FABT), as one of the most promising derivatives from the N-substituted 2-amino-5-(2,4-dihydroxyphenyl)-1,3,4-thiadiazole set, have been continued. The tested compound inhibited proliferation of tumor cells derived from cancers of nervous system (medulloblastoma/rhabdosarcoma, neuroblastoma, and glioma) and peripheral cancers including colon adenocarcinoma and lung carcinoma. The anticancer effect of FABT was attributed to decreased cell division and inhibited cell migration. Furthermore, in anticancer concentrations it exerted a trophic effect in neuronal cell culture and had no influence on viability of normal cells including astrocytes, hepatocytes, and skin fibroblasts. Moreover, a prominent neuroprotective activity of FABT was observed in the neuronal cultures exposed to neurotoxic agents like serum deprivation and glutamate. To determine probability of tautomeric transition and indicate potential sites of interactions of FABT molecule with the receptor, quantum-chemical calculations with the ab initio Hartree-Fock model were made.     

Tautomeric forms study of 1H-(2′-pyridyl)-3-methyl-5-hydroxypyrazole and 1H-(2′-pyridyl)-3-phenyl-5-hydroxypyrazole. Synthesis,structure, and cytotoxic activity of their complexes with palladium(II) ions

In this article the synthesis of new 1H-(2′-pyridyl)-3-methyl-5-hydroxypyrazole and 1H-(2′-pyridyl)-3-phenyl-5-hydroxypyrazole complexes with palladium(II) ions is reported. The structures of obtained compounds have been characterized by X-ray crystallography and DFT (density functional theory) calculations. The cytotoxicity of complexes and ligands has been examined for two human leukemia cell lines (HL-60 and NALM-6) and one human melanoma cell line (WM-115). The palladium(II) complex with 1H-(2′-pyridyl)-3-phenyl-5-hydroxypyrazole has been shown to possess greater activity than carboplatin against the WM-115 melanoma cell line. Additionally, the ligands’ tautomeric forms existence in different solvents (chloroform, methanol, DMSO) has been characterized by ¹H nuclear magnetic resonance (NMR) analysis and DFT calculations. The obtained results have been compared with those from other studies of similar compounds.     

Interaction of nucleic acids and glycans

Spectrophotometric analysis and dot-hybridization have shown that amylose forms complexes with polypyrimidines (poly dC), while polyuronides form complexes with polypurines (poly dA). In addition, the formation of complexes genomic thymus DNA-hyaluronic acid has been observed. A certain role in the mechanism of NA-polysaccharide interactions can be played by the links between purines and the carboxylic group of hexuronic acid residue, as well as between pyrimidines and the hydroxymethyl group of hexose residue. The quantum-chemical calculations showed that, between nitric bases of DNA and the carboxyl groups of hexuronic acids or the hydroxymethyl group of hexose, hydrogen bonds can be formed the energy of which is comparable with that in the complementary AT and CG pairs. The strength of these bonds is unequal: carboxyl groups form stronger hydrogen bonds with purines and weaker bonds with pyrimidines. The hydroxymethyl group, on the contrary, forms stronger hydrogen bonds with pyrimidines and weaker bonds with purines. The quantum-chemical modeling shows that, in the complementary pairs purin-uronic acid and pyrimidine-hexose, hydrogen bonds are produced that form a binary chain nucleic acid-polysaccharide. The data obtained suggest the existence of template synthesis of GAG polysaccharide fragments with the participation of NA.     

Tautomeric energetics of xanthine oxidase substrates: xanthine, 2-oxo-6-methylpurine, and lumazine

The stability of the tautomers of each of the three important substrates of xanthine oxidase, xanthine, 2-oxo-6-methylpurine, and lumazine, was examined by quantum mechanical calculations. The geometries of these tautomers were optimized at the AM1, Hartree-Fock (HF/6-31G), and hybrid Hartree-Fock/density functional theory (B3LYP/6-31G(d)) levels of theory. The single point energies of some of the more stable tautomers for each of the substrates were calculated at the B3LYP/6-311 +G(2d,p) level of theory. The Conductor Polarized Continuum Model (CPCM) was used to evaluate the solvent effects on the relative stabilities of these tautomers. The calculations clearly identify the lowest energy tautomeric form for xanthine and lumazine. On the other hand, there appear to be three tautomers for 2-oxo-6-methylpurine, with only minor energetic differences in vacuo. In water, however, only one of them predominates. The lowest energy tautomers presumably represent the predominant tautomeric forms at the molybdenum center of xanthine oxidase during catalysis. Implications of these computational results are discussed in the context of enzyme catalysis.     

New N-substituted hydrazones,derivatives of uridyl aldehyde

N-substituted isomeric hydrazones of uridyl aldehyde have been synthesized. The occurrence of the dominant E isomers with respect to the azomethine group was confirmed by means of NMR spectroscopy. Synthesized hydrazones feature an acetonide moiety as a protection of two hydroxyl groups on the ribose part. The attempt to remove the protecting group resulted in an azo-hydrazone tautomeric mixture. The described compounds may be valuable chiral ligands for metal chelation. Assessment of manganese(II) ion affinity to one selected hydrazone was performed.     

Elucidation of the chemistry of enzyme-bound thiamin diphosphate prior to substrate binding: defining internal equilibria among tautomeric and ionization states

Both solution and crystallographic studies suggest that the 4'-aminopyrimidine ring of the thiamin diphosphate coenzyme participates in catalysis, likely as an intramolecular general acid-base catalyst via the unusual 1',4'-iminopyrimidine tautomer. It is indeed uncommon for a coenzyme to be identified in its rare tautomeric form on its reaction pathways, yet this has been possible with thiamin diphosphate, in some cases even in the absence of substrate [Nemeria, N., Chakraborty, S., Baykal, A., Korotchkina, L., Patel, M. S., and Jordan, F. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 78-82.]. The ability to detect both the aminopyrimidine and iminopyrimidine tautomeric forms of thiamin diphosphate on enzymes has enabled us to assign the predominant tautomeric form present in individual intermediates on the pathway. Herein, we report the pH dependence of these tautomeric forms providing the first data for the internal thermodynamic equilibria on thiamin diphosphate enzymes for the various ionization and tautomeric forms of this coenzyme on four enzymes: benzaldehyde lyase, benzoylformate decarboxylase, pyruvate oxidase, and the E1 component of the human pyruvate dehydrogenase multienzyme complex. Evidence is provided for an important function of the enzyme environment in altering both the ionization and tautomeric equilibria on the coenzyme even prior to addition of substrate. The pKa for the 4'-aminopyrimidinium moiety coincides with the pH for optimum activity thereby ensuring that all ionization states and tautomeric states are accessible during the catalytic cycle. The dramatic influence of the protein on the internal equilibria also points to conditions under which the long-elusive ylide intermediate could be stabilized.     

Tautomerism in 8-Nitroguanosine Studied by NMR and Theoretical Calculations

The guanine base in DNA, due to its low oxidation potential, is particularly sensitive to chemical modifications. A large number of guanine lesions have been characterized and studied in some detail due to their relationship with tissue inflammations. Nevertheless, one example of these lesions is the formation of 8-nitro-guanosine, but the NMR data of this compound was only partially interpreted. A comprehensive study of the two possible tautomeric forms, through a detailed characterization of this compound, has implications for its base pairing properties. The target compound was obtained through a synthetic sequence of five steps, where all intermediates were fully characterized using spectral data. The analysis of the two tautomers was then evaluated through NMR spectroscopy and theoretical calculations of the chemical shifts and NH coupling constants, which were also compared with the data from guanosine.     

Effects of a 8-oxoadenosine incorporation on quadruplex structures: thermal stabilities and structural studies

The effects of incorporation of 8-oxoadenosine in two different truncations of human telomeric sequence forming quadruplex structures are reported. In order to characterise their structures, a combination of NMR and UV spectroscopy and computational techniques were used. Both oligonucleotides have been found to form fourfold symmetric quadruplex structures. As a tautomeric equilibrium between keto and enol forms of 8-oxoadenosine may establish in solution and intrinsic stabilities effects, such as internal H-bonds, for example, may determine the predominance of some particular tautomer, molecular modelling studies were performed on quadruplex structures containing both the tautomeric forms. Both molecules resulted to be thermally less stable than the natural.     

Electron-topological, energetic and π-electron delocalization analysis of ketoenamine-enolimine tautomeric equilibrium

The ketoenamine-enolimine tautometic equilibrium has been studied by the analysis of aromaticity and electron-topological parameters. The influence of substituents on the energy of the transition state and of the tautomeric forms has been investigated for different positions of chelate chain. The quantum theory of atoms in molecules method (QTAIM) has been applied to study changes in the electron-topological parameters of the molecule with respect to the tautomeric equilibrium in intramolecular hydrogen bond. Dependencies of the HOMA aromaticity index and electron density at the critical points defining aromaticity and electronic state of the chelate chain on the transition state (TS), OH and HN tautomeric forms have been obtained.     

Assessment of antidotal efficacy of cholinesterase reactivators against paraoxon: In vitro reactivation kinetics and physicochemical properties

The search of proficient oximes as reactivators of irreversibly inhibited-AChE by organophosphate poisoning necessitates an appropriate assessment of their physicochemical properties and reactivation kinetics. Therefore, herein acid dissociation constant; pK_a, lipophilicity; log P, polar surface area, hydrogen bond donor and acceptor counts of structurally different oximes (two tertiary oximes and thirteen pyridinium aldoxime derivatives) have been evaluated. The experimentally obtained data for pK_a has been comparatively analyzed by using non-linear regression. Further the tested oximes were screened through in vitro reactivation kinetics against paraoxon-inhibited AChE. The pK_a values of all the examined oximes were within the range of 7.50–9.53. pK_a values of uncharged and mono-pyridinium oximes were in good correlation with their reactivation potency. The high negative log P values of pyridinium oxime reactivators indicate their high hydrophilic character; hence oximes with improved lipophilicity should be designed for the development of novel and more potent antidotes. Propane and butane linked oximes were superior reactivators than xylene linked bis-oxime reactivators. It is concluded from the present study that pK_a value is not only ruled by the position of oximino functionality in the pyridinium ring, but also by the position of linker. Although, pyridinium oximes are proved to be better reactivators but their lipophilicity has to be improved.     

Variations of the tautomeric preferences and π-electron delocalization for the neutral and redox forms of purine when proceeding from the gas phase (DFT) to water (PCM)

Quantum-chemical calculations were performed for all possible nine neutral tautomers of purine and their oxidized and reduced forms in water {PCM//DFT(B3LYP)/6?311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6?311+G(d,p)}. PCM hydration influences geometries, π-electron delocalization, and relative energies of purine tautomers in different ways. Generally, the harmonic oscillator model of electron delocalization (HOMED) indices increase when proceeding from the gas phase to aequeous solution for the neutral and redox forms of purine. Their changes for the neutral and oxidized tautomers are almost parallel to the relative energies showing that aromaticity plays an important role in the tautomeric preferences. Tautomeric stabilities and tautomeric preferences vary when proceeding from the gas phase to water indicating additionally that intra- and intermolecular interactions affect tautomeric equilibria. The tautomeric mixture of neutral purine in the gas phase consists mainly of the N9H tautomer, whereas two tautomers (N9H and N7H) dominate in water. For oxidized purine, N9H is favored in the gas phase, whereas N1H in water. A gain of one electron dramatically changes the relative stabilities of the CH and NH tautomers that C6H and C8H dominate in the tautomeric mixture in the gas phase, whereas N3H in water. These variations show exceptional sensitivity of the tautomeric purine system on environment in the electron-transfer reactions.