Synthesis of acyclic and macrocyclic analogs of Di-, Tri-, and tetranucleotides

Compounds consisting of two or three uracil fragments were synthesized by reaction of methyl-substituted uracil sodium salts with 1-(6-bromohexyl)-3,6-dimethyluracil or 1,6-dibromohexane. Treatment of these compounds with paraformaldehyde gave the corresponding pyrimidinophanes and acyclic compounds in which the uracil fragments are linked through methylene bridges. Uracil derivatives having no substituent on N³ were synthesized by reactions of silylated uracils with 1,3-bis(6-bromohexyl)uracil or 4,4′-(6-bromohexyloxy)diphenylmethane. The acyclic compound was converted into pyrimidinophane containing uracil fragments with N³H groups. A trinucleotide analog including uracil and two adenine fragments was synthesized from 1,3-bis(6-bromohexyl)uracil.     

Barrier-free intermolecular proton transfer induced by excess electron attachment to the complex of alanine with uracil

The photoelectron spectrum of the uracil-alanine anionic complex (UA)(-) has been recorded with 2.540 eV photons. This spectrum reveals a broad feature with a maximum between 1.6 and 2.1 eV. The vertical electron detachment energy is too large to be attributed to an (UA)(-) anionic complex in which an intact uracil anion is solvated by alanine, or vice versa. The neutral and anionic complexes of uracil and alanine were studied at the B3LYP and second-order M?ller-Plesset level of theory with 6-31++G(*) (*) basis sets. The neutral complexes form cyclic hydrogen bonds and the three most stable neutral complexes are bound by 0.72, 0.61, and 0.57 eV. The electron hole in complexes of uracil with alanine is localized on uracil, but the formation of a complex with alanine strongly modulates the vertical ionization energy of uracil. The theoretical results indicate that the excess electron in (UA)(-) occupies a pi(*) orbital localized on uracil. The excess electron attachment to the complex can induce a barrier-free proton transfer (BFPT) from the carboxylic group of alanine to the O8 atom of uracil. As a result, the four most stable structures of the uracil-alanine anionic complex can be characterized as a neutral radical of hydrogenated uracil solvated by a deprotonated alanine. Our current results for the anionic complex of uracil with alanine are similar to our previous results for the anion of uracil with glycine, and together they indicate that the BFPT process is not very sensitive to the nature of the amino acid's hydrophobic residual group. The BFPT to the O8 atom of uracil may be relevant to the damage suffered by nucleic acid bases due to exposure to low energy electrons.     

Sensing System Integrating Lanthanum Hydroxide Nanowires with Copper(II) Ion for Uracil and its Application

Abstract

A sensing system for uracil was constituted by using lanthanum hydroxide nanowires (LNW) as a modifier to obtain LNW modified carbon paste electrode (LNW/CPE) and by introducing copper(II) ion into supporting electrolyte to transform electroinactive uracil to electroactive uracil‐Cu(II) complex. The voltammetric behaviors of uracil in the presence of Cu(II) ion at LNW/CPE were investigated. A reduction peak of the uracil‐Cu(II) complex at ?0.18 V was the two‐electron reduction of Cu(II) ion in the uracil‐Cu(II) complex; while a new oxidation peak at 0.22 V was the one‐electron oxidation of the uracil‐Cu(I) complex. Additionally, the voltammetric responses of all the complexes at LNW/CPE were more sensitive than that at carbon and multiwall carbon nanotube paste electrodes, which resulted from both the large surface effect of LNW and the chemical coordination of uracil with La(III) ion in LNW. With the sensitive oxidation peak of the uracil‐Cu(I) complex at LNW/CPE, a linear range of 4.0×10^?9?3.0×10^?8 mol/l for uracil was obtained along with a detection limit of 2.0×10^?10 mol/l. The proposed system was evaluated by the determination of uracil derivatives, anticancer drug 5‐flurouracil, in pharmaceutical preparations.     

An Efficient Approach for the Synthesis of 1,2,3‐Triazole Moiety to Generate Uracil Molecular Architectures Through Cu‐Catalyzed Azide–Alkyne Cycloaddition

A simple and efficient pathway to tether conjugates of monosaccharides or aromatic moieties to uracil establishing a 1,2,3‐triazole linker via click chemistry was reported. The reaction of arylimines of 5‐amino uracil with propargyl bromide in a basic medium gave a di‐propargylated uracil. The latter compound was converted into molecular architectures containing bis‐1,2,3‐triazole rings through Cu‐catalyzed 1,3‐cycloaddition reaction with different azides. The same arylimine of 5‐amino uracil yielded different products under reflux with propargyl bromide in acetonitril with the majority to 6‐propargylated‐5‐amino uracil.     

The structure of uracil: a laser ablation rotational study

The jet-cooled rotational spectrum of uracil has been investigated using laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy. The quadrupole structure originated by the two 14N nuclei of uracil has been completely resolved and assigned. This provides a definitive method to establish the pyrrolic or pyrimidinic nature of the N nuclei and allows us to conclude that the observed tautomer of uracil in the gas phase is the diketo form. From the rotational constants of the isotopic species detected, a structure of uracil has been determined.     

Tautomerism of uracil probed via infrared spectroscopy of singly hydrated protonated uracil

Tautomerism of the nucleobase uracil is characterized in the gas phase through IR photodissociation spectroscopy of singly hydrated protonated uracil created with tandem mass spectrometric methods in a commercially available Fourier transform ion cyclotron resonance mass spectrometer. Protonated uracil ions generated by electrospray ionization are re-solvated in a low-pressure collision cell filled with a mixture of water vapor seeded in argon. Their structure is investigated by IR photodissociation spectroscopy in the NH and OH stretching region (2500-3800 cm(-1)) with a tabletop IR laser source and in the 1000-2000 cm(-1) range with a free-electron laser. In both regions the IR photodissociation spectrum exhibits well-resolved spectral signatures that point to the presence of two different types of structure for monohydrated protonated uracil, which result from the two lowest-energy tautomers of uracil. Ab initio calculations confirm that no water-catalyzed tautomerization occurs during the re-solvation process, indicating that the two protonated forms of uracil directly originate from the electrospray process.     

Partial Molar Volumes of Uracil,Thymine, Adenine in Water and of Adenine in Aqueous Solutions of Uracil and Thymine

The partial molar volumes of uracil, thymine and adenine in water and adenine in aqueous solutions of uracil and thymine, at fixed composition, were determined over a range of temperatures. The partial molar volumes of adenine in aqueous uracil and thymine are less than in pure water.     

Lp...π Interactions involving π-systems with different degrees of electron density delocalization: uracil and isocyanurate

A comparative analysis of non-covalent interactions in the crystals of uracil and isocyanurate derivatives was performed. Most of interactions involving the uracil moiety are formed via π...π-type overlap, but Lp...π-type interactions also occur in some crystals. A comparison of the lone pair—π-system interactions showed that the energy of these interactions in uracil derivatives is lower than that in isocyanurate derivatives, which is attributed to a lower positive charge on the uracil moiety.     

Solvation Structure of Uracil in Ionic Liquids

The local solvation environment of uracil dissolved in the ionic liquid 1‐ethyl‐3‐methylimidazolium acetate has been studied using neutron diffraction techniques. At solvent:solute (ionic liquid:uracil) ratios of 3:1 and 2:1, little perturbation of the ion–ion correlations compared to those of the neat ionic liquid are observed. We find that solvation of the uracil is driven predominantly by the acetate anion of the solvent. While short distance correlations exist between uracil and the imidazolium cation, the geometry of these contacts suggest that they cannot be considered as hydrogen bonds, in contrast to other studies by Araújo et al. (J. M. Araújo, A. B. Pereiro, J. N. Canongia‐Lopes, L. P. Rebelo, I. M. Marrucho, J. Phys. Chem. B 2013, 117, 4109–4120 ). Nevertheless, this combination of interactions of the solute with both the cation and anion components of the solvents helps explain the high solubility of the nucleobase in this media. In addition, favourable uracil–uracil contacts are observed, of similar magnitude to those between cation and uracil, and are also likely to aid dissolution.     

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.     

Molecular orbital theory of the hydrogen bond. 26. The hydration of uracil

Ab initio SCF calculations with the STO -3G basis set have been performed to determine the structure and stability of a 6:1 water:uracil heptamer in which water molecules are hydrogen bonded to uracil at each of the six hydrogen-bonding sites in the uracil molecular plane. The structure of the heptamer describes a stable arrangement of these six water molecules, which are the primary solvent molecules in the first solvation shell, and is suggestive of the arrangement of secondary solvent molecules in that shell in the nonpolar region of the uracil molecular plane. The stabilization energy of the heptamer is 49.6 kcal/mol, or 8.3 kcal/mol per water molecule. The hydrogen bonds between uracil and water are the primary factor in the stabilization of the complex, although water–water interactions and nonadditivity effects are also significant.     

A convenient method for N-1 arylation of uracil derivatives

1-(4-Nitrophenyl)- and 1-(2,4-dinitrophenyl)uracil derivatives have been obtained by direct arylation of uracil and its 5-substituted derivatives using 1-fluoro-4-nitrobenzene or 1-fluoro-2,4-dinitrobenzene in the presence of a base. The application of the newly obtained uracil derivatives in further synthesis is also presented.     

Effects of microsolvation on uracil and its radical anion: uracil(H2O)n (n = 1-5)

Microsolvation effects on the stabilities of uracil and its anion have been investigated by explicitly considering the structures of complexes of uracil with up to five water molecules at the B3LYPDZP++ level of theory. For all five systems, the global minimum of the neutral cluster has a different equilibrium geometry from that of the radical anion. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of uracil are predicted to increase gradually with the number of hydrating molecules, qualitatively consistent with experimental results from a photodetachment-photoelectron spectroscopy study [J. Schiedt et al., Chem. Phys. 239, 511 (1998)]. The trend in the AEAs implies that while the conventional valence radical anion of uracil is only marginally bound in the gas phase, it will form a stable anion in aqueous solution. The gas-phase AEA of uracil (0.24 eV) was higher than that of thymine by 0.04 eV and this gap was not significantly affected by microsolvation. The largest AEA is that predicted for uracil(H2O)5, namely, 0.96 eV. The VDEs range from 0.76 to 1.78 eV.     

Determination of creatinine-related urinary uracil excretion in children by high-performance liquid chromatography

Excretion rates of uracil and thymine in children (n = 140) and circadian rhythms of urinary uracil excretion (n = 9) were investigated by reversed-phase high-performance liquid chromatography with ultraviolet detection. Excretion values were related to urinary creatinine determined by Jaffé's method. Creatinine-related uracil excretion was not dependent on age or sex. The values seemed to be distributed according to a Gaussian graph in both school children and those in hospital. The intra-individual range was 1.32-23.70 mg uracil per g creatinine over a four-day period in one subject. Uracil excretion seems to be somewhat lower during the night.     

Combinative improving effect of increased solubility and the use of absorption enhancers on the rectal absorption of uracil in beagle dogs

An improvement of the rectal absorption of uracil was examined by the application of absorption enhancers in addition to the increased solubility of uracil. Uracil was ground with additives such as MgO, sodium 2,6-dihydroxybenzoate, human serum albumin or hydroxypropylmethylcellulose acetate succinate. Aqueous, oily and powdery formulations, which consisted of the ground mixtures, nicotinamide, urea and absorption enhancers such as polyoxyethylene (23) cetylether (BC-23) or sodium caprate, were prepared. Uracil solubility in the aqueous formulations was increased about 4-13 times that in the corresponding control formulations. When rectally administered to beagle dogs, marked increases in the plasma uracil level were observed in some of the cases of aqueous and oily formulations. In the powdery formulations and formulations containing macromolecular additives, however, absorption improvements was not observed. The results indicated that an improvement in the absorption of uracil was caused by the combinative improving effect of the increased uracil solubility and the promoting effect of absorption enhancers.     

Anti-HIV Active Naphthyl Analogues of HEPT and DABO

 5-Isopropyl-6-naphthyl uracil and 5-isopropyl-6-naphthyl-2-thiouracil were alkylated to give N-1-(ethoxymethyl and methylthiomethyl) uracil and S²-cyclohexyl-thiouracil, respectively. 5-Ethyl-6-naphthyl uracil and 5-ethyl-6-naphthyl-2-thiouracil afforded N-1-(ethoxymethyl, methoxy-methyl, methylthiomethyl, acetoxyethoxy methyl and hydroxyethoxy methyl) uracil and S²-((2,2- diethoxyethyl), methoxycarbonylmethyl, ethoxycarbonylpropyl, methylthiomethyl, ethoxymethyl, methyl and cyclohexyl)-thiouracil upon alkylation.     

Thermodynamics and the mechanism of interaction of uracil with amino acids in water

Interaction of most of the side groups of amino acids with uracil and their dehydration do not contribute significantly to the pair interaction coefficients. It has been suggested that the interaction between the terminal groups of amino acids and the side groups of uracil (NH, CO) occurs by the acid-base mechanism. The possibility was found of formation of uracil+l-proline associates, owing to favorable configurations of the components, uracil+l-tryptophan associates, owing to π-π electronic interaction between their aromatic rings, and uracil+l-lysine: HCl, owing to the side ammonium group in amino acid. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 932–934, May, 1997.     

THE MECHANISM OF PHOTOCHEMICAL ADDITION OF CYSTEINE TO URACIL AND FORMATION OF DIHYDROURACIL

Abstract— A proposed mechanism for the photochemical addition of L -cysteine to uracil with the concurrent formation of dihydrouracil is shown to proceed through the triplet excited state of uracil which can abstract hydrogen atoms from cysteine to form dihydrouracil. This triplet state is the same one as that leading to photodimerization. The thiyl radicals generated add to ground state uracil molecules. The data permit a re-evaluation of the quantum yield for intersystem crossing of uracil in water which shows dimerization in aqueous solution to have a maximum efficiency of 56 per cent. The formation of the cross-adduct and dihydrouracil may be sensitized but the efficiency of the reaction is related to the ability of the sensitizer to be photoreduced and not to its triplet energy.     

Carbon nanotube-nucleobase hybrids: nanorings from uracil-modified single-walled carbon nanotubes

Single‐walled carbon nanotubes (SWCNTs) have been covalently functionalized with uracil nucleobase. The hybrids have been characterized by using complementary spectroscopic and microscopic techniques including solid‐state NMR spectroscopy. The uracil‐functionalized SWCNTs are able to self‐assemble into regular nanorings with a diameter of 50–70 nm, as observed by AFM and TEM. AFM shows that the rings do not have a consistent height and thickness, which indicates that they may be formed by separate bundles of CNTs. The simplest model for the nanoring formation likely involves two bundles of CNTs interacting with each other via uracil–uracil base‐pairing at both CNT ends. These nanorings can be envisaged for the development of advanced electronic circuits.     

Anti-HIV Active Naphthyl Analogues of HEPT and DABO

Summary.  5-Isopropyl-6-naphthyl uracil and 5-isopropyl-6-naphthyl-2-thiouracil were alkylated to give N-1-(ethoxymethyl and methylthiomethyl) uracil and S²-cyclohexyl-thiouracil, respectively. 5-Ethyl-6-naphthyl uracil and 5-ethyl-6-naphthyl-2-thiouracil afforded N-1-(ethoxymethyl, methoxy-methyl, methylthiomethyl, acetoxyethoxy methyl and hydroxyethoxy methyl) uracil and S²-((2,2- diethoxyethyl), methoxycarbonylmethyl, ethoxycarbonylpropyl, methylthiomethyl, ethoxymethyl, methyl and cyclohexyl)-thiouracil upon alkylation. Received September 25, 2001. Accepted (revised) December 3, 2001