Relative stability of keto-enol tautomers in 5,6-substituted uracils: Ab initio, DFT and PCM study

New Polymorphic Modifications of 6-Methyluracil: An Experimental and Quantum Chemical Study

Polymorphism of 6-methyluracil, which affects the regulation of lipid peroxidation and wound healing, has been studied by experimental and quantum chemical methods. Two known polymorphic modifications and two new crystalline forms were crystallized and characterized by single crystal and powder X-ray diffraction (XRD) methods as well as by the differential scanning calorimetry (DSC) method and infrared (IR) spectroscopy. The calculations of pairwise interaction energies between molecules and lattice energies in periodic boundary conditions have shown that the polymorphic form 6MU_I used in the pharmaceutical industry and two new forms 6MU_III and 6MU_IV, which can be formed due to temperature violations, may be considered as metastable. The centrosymmetric dimer bound by two N-H···O hydrogen bonds was recognized as a dimeric building unit in all of the polymorphic forms of 6-methyluracil. Four polymorphic forms have a layered structure from the viewpoint of interaction energies between dimeric building units. The layers parallel to the (100) crystallographic plane were recognized as a basic structural motif in the 6MU_I, 6MU_III, and 6MU_IV crystals. In the 6MU_II structure, a basic structural motif is a layer parallel to the (001) crystallographic plane. The ratio between the interaction energies within the basic structural motif and between neighboring layers correlates with the relative stability of the studied polymorphic forms. The most stable polymorphic form 6MU_II has the most anisotropic "energetic" structure, while the interaction energies in the least stable form 6MU_IV are very close in various directions. The modeling of shear deformations of layers in the metastable polymorphic structures has not revealed any possibility of these crystals to be deformed under external mechanical stress or pressure influence. These results allow the use of metastable polymorphic forms of 6-methyluracil in the pharmaceutical industry without any limitations.

Solvent and temperature effects on the tautomerization of a carbonitrile molecule: A conductor-like polarizable continuum model (CPCM) study

This research examined the effects of solvent polarity and temperature on the tautomerization of a carbonitrile molecule at CAM-B3LYP/6-311G (d,p) level of theory. The selected solvents were n-hexane, diethyl ether, pyridine, ethanol, methanol, and water. The solvent effects were examined by the self-consistent reaction field theory (SCRF) based on conductor-like polarizable continuum model (CPCM). The solvent effects were explored on the energy barrier, frontier orbitals energies, and HOMO-LUMO gap. Dependencies of thermodynamic parameters (ΔG and ΔH) on the dielectric constants of solvents were also tested. Specifically, the temperature dependencies of the thermodynamics parameters were studied within 100–1000 K range. The rate constant of the tautomerism reaction was computed from 300 to 1200 K, in the gas phase.

RNA Editing of the Human DNA Glycosylase NEIL1 Alters Its Removal of 5-Hydroxyuracil Lesions in DNA

Editing of the pre-mRNA of the DNA repair glycosylase NEIL1 results in substitution of a Lys with Arg in the lesion recognition loop of the enzyme. Unedited (UE, Lys242) NEIL1 removes thymine glycol lesions in DNA ∼30 times faster than edited (Ed, Arg242) NEIL1. Herein, we evaluated recognition and excision mediated by UE and Ed NEIL1 of 5-hydroxyuracil (5-OHU), a highly mutagenic lesion formed via oxidation of cytosine. Both NEIL1 isoforms catalyzed low levels of 5-OHU excision in single-stranded DNA, bubble and bulge DNA contexts and in duplex DNA base paired with A. Removal of 5-OHU in base pairs with G, T, and C was found to be faster and proceed to a higher overall extent with UE than with Ed NEIL1. In addition, the presence of mismatches adjacent to 5-OHU magnified the hampered activity of the Ed isoform. However, Ed NEIL1 was found to exhibit higher affinity for 5-OHU:G and 5-OHU:C duplexes than UE NEIL1. These results suggest that NEIL1 plays an important role in detecting and capturing 5-OHU lesions in inappropriate contexts, in a manner that does not lead to excision, to prevent mutations and strand breaks. Indeed, inefficient removal of 5-OHU by NEIL1 from 5-OHU:A base pairs formed during replication would thwart mutagenesis. Notably, nonproductive engagement of 5-OHU by Ed NEIL1 suggests the extent of 5-OHU repair will be reduced under cellular conditions, such as inflammation, that increase the extent of NEIL1 RNA editing. Tipping the balance between the two NEIL1 isoforms may be a significant factor leading to genome instability.

Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives

We report on the density functional theory (DFT) modelling of structural, energetic and NMR parameters of uracil and its derivatives (5-halogenouracil (5XU), X = F, Cl, Br and I) in vacuum and in water using the polarizable continuum model (PCM) and the solvent model density (SMD) approach. On the basis of the obtained results, we conclude that the intramolecular electrostatic interactions are the main factors governing the stability of the six tautomeric forms of uracil and 5XU. Two indices of aromaticity, the harmonic oscillator model of aromaticity (HOMA), satisfying the geometric criterion, and the nuclear independent chemical shift (NICS), were applied to evaluate the aromaticity of uracil and its derivatives in the gas phase and water. The values of these parameters showed that the most stable tautomer is the least aromatic. A good performance of newly designed xOPBE density functional in combination with both large aug-cc-pVQZ and small STO(1M)-3G basis sets for predicting chemical shifts of uracil and 5-fluorouracil in vacuum and water was observed. As a practical alternative for calculating the chemical shifts of challenging heterocyclic compounds, we also propose B3LYP calculations with small STO(1M)-3G basis set. The indirect spin-spin coupling constants predicted by B3LYP/aug-cc-pVQZ(mixed) method reproduce the experimental data for uracil and 5-fluorouracil well.

Luminescent and DFT Study of Keto-Enol Tautomers of 5-Fluorouracil and Its Derivatives in Aqueous Solutions

Fluorescence (FL) spectra were recorded and identified for the following 5-fluorouracil (FU) tautomers: 5-fluoropyrimidine-2,4(1H,3H)-dione (A), 5-fluoro-2-hydroxypyrimidine-4(3H)-one (B), and 5-fluoro-4-hydroxypyrimidine-2(1H)-one (D), as well as the corresponding tautomers A and D of 1-(tetrahydrofuranyl-2)-5-fluorouracil and 1-methyl-5-fluorouracil, tautomers A and B of 3-methyl-5-fluorouracil, and the diketo tautomer of 1,3-dimethyl-5-fluorouracil. It was shown that the FL of rare tautomers of FU derivatives occurs by the excitation of uracil homoassociates followed by intramolecular proton transfer (IPT), formation of a pair of rare tautomers, and radiative deactivation of one of them. The FL quantum yields φ_i were estimated. In the case of rare tautomers, the φ_i value includes the probability of IPT in the homoassociate, and density functional theory calculations in the TPSSTPSS/6-311+G(d,p) approximation were used to determine the relative energies of tautomers, associated FU forms, and their spectral properties that agree with the observed luminescence pattern.

The effect of water-mediated catalysis on the intramolecular proton-transfer reactions of the isomers of 5-chlorouracil: a theoretical study

The geometrical structures and thermal energies (E), enthalpies (H) and Gibbs free energies (G) of 13 isomers of 5-chlorouracil (5ClU) in the gas and water phases were investigated using the density functional theory (DFT) method at the M06-2X/6-311++g(3df,3pd) level. The isomers of 5ClU can be microhydrated at different molecular target sites. The mono- and dihydrated forms are the most stable in both the gas and water phases, and, because of the intermolecular interactions, the hydrations lead to a degree of change in the stability trend. Two types of isomerizations were considered: the internal H-O bond rotations in which the H atom rotates 180° around the C-O bond and the intramolecular proton-transfer reactions in which an H atom is transferred between an O atom and a neighbouring N atom. The forward and backward energy barriers for isomerizations of nonhydrated 5ClU were calculated. In addition, 16 optimized transition-state structures for water-mediated catalysis on isomerizations of 5ClU were investigated. The forward and backward proton-transfer energy barriers of water-mediated catalysis on isomerizations of 5ClU were obtained. The results indicate that the catalytic effect of two H₂O molecules is much greater than that of one H₂O molecule in isomerizations of 5ClU.

Co-crystallization and polymorphic behaviour of 5-fluorouracil

Hydrogen donors and acceptors in 5-fluorouracil allow the formation of co-crystalline compounds with nontoxic co-formers of the GRAS list and an alternative target-oriented synthon approach from methanol or ethanol to form II of 5-fluorouracil is presented.

Relative Populations of Some Tautomeric Forms of 2'-Deoxyguanosine-5-Fluorouridine Mismatch

The importance of the 2'-deoxyguanosine-uridine mispair as the most occurring mismatch in transcriptional studies of RNAs from DNAs is multiplied when 5-halo-substituted uridine species cause a serious increase in the probability of its occurrence. Many studies relate this higher probability to the existence of possible tautomeric and ionic forms of its constituent bases. According to these statements, relative populations of mismatches between 5-fluorouridine and both keto and enol forms of 2'-deoxyguanosine are computed by using a conformational search. In order to have a complete scan of all of the highly probable conformers in a moderate computational time, an extensive conformational search methodology is employed here, which benefits from the advantages of both the molecular dynamics simulations and quantum mechanics calculations. The population of an enolic tautomer of normal wobble orientation is about 0.057% of that of its keto tautomer, whereas the population of an enolic tautomer of reverse wobble orientation is about 0.0054% of that of its keto tautomer. Totally, the reverse wobble orientation is about six times more populated than the normal wobble orientation. Calculated populations are in good agreement with experimental populations of closely related compounds. The reliability of the applied methodology is certified, in part, by a good agreement obtained between some experimental data and corresponding Boltzmann-weighted average data of most probable conformers such as NMR parameters. The validation of this methodology is certified with high accuracy by applying it on the substituted diuridine pairs, where experimental populations are available. Not only are the calculated populations and NMR parameters of this test in very good agreement with the experimental data, but also they are free of the ambiguities mentioned by experimentalists.

The evaluation of 5-amino- and 5-hydroxyuracil derivatives as potential quadruplex-forming agents

5-Substituted uracils (NH₂ or OH groups in position 5) have been examined theoretically and experimentally as potential building blocks in quadruplex structures. Our high level Density Functional Theory (DFT) calculations showed that the tetramer formation and stacking energies for 5-substituted uracils are similar to the energies of purine-based xanthine (X) or guanine (G) structures. As tetrads of 5-substituted uracils cover almost exactly the same area as purine tetrads, mixed tetrads or quadruplex structures based on X or G and 5-substituted uracil motifs are possible. According to the calculations, 5-hydroxyuracil-based structures are the best candidates for experimental implementation which was corroborated by the existence of higher complexes in the mass spectra of 1-benzyl-5-hydroxyuracil. These pyrimidine-based molecules can be used as efficient building blocks in different applications including aptamers, bio-sensors or - taking into account the larger cavity in the central region of 5-hydroxyuracil structures - as an artificial ion channel.

Theoretical Models for Quantitative Description of the Acid-Base Equilibria of the 5,6-Substituted Uracils

The acidities of 18 5,6-substituted uracils have been numerically estimated as pK_a values in terms of three theoretical models. The first scheme includes the calculation of the gas-phase acidity of uracil with the G3MP2B3 method and taking into account the solvent effect using the polarizable continuum approximation PCM(SMD)-TPSS/aug-cc-pVTZ. The second model is one step and implies calculation of the free Gibbs energies of the hydrate complex of uracil (and its anion) with 5 water molecules by the TPSS/aug-cc-pVTZ method. This model accounts for the solvent effect corresponding to both specific and nonspecific solvation. The third scheme required high time and computational resources and includes the strong features of the two previous schemes. Here, the theoretical estimation of pK_a is performed by the CBS-QB3 composite method. As in the second approach, both specific (as pentahydrate) and nonspecific solvent effects are determined. We have analyzed the advantages and model restrictions of the considered schemes for the pK_a calculations. All models have systematic errors, which have been corrected with the linear empirical regression relations. In the presented model, the absolute mean deviations of the pK_a values of uracils dissociating via the N1-H bonds diminish to 0.25, 0.28, and 0.23 pK_a units (respectively, for I, II, and III models), which corresponds to ∼0.3 kcal/mol on the energy scale. The applicability of our computational schemes to uracils dissociating via N3-H, O-H (orotic acids) and C-H bonds is discussed.

Controlled stabilization of anionic forms of the uracil derivatives: A DFT study

Relative stabilities of the N1/N3/О5/О6 anions of 42 substituted uracils in gas phase and aqueous solutions have been theoretically studied using approximation IEFPCM (SMD) - TPSS/aug-cc-pVTZ. The specific solvation of uracil and its anions has been simulated with the first hydrate shell made up with 5 water molecules. The nonspecific solvation has been accounted in terms of the SMD model. We have found a series of relative stability under conditions of both specific and nonspecific hydration. The series is ranked according to the increase of the relative stability of the N3 anion. In gas phase, the N1 anion is significantly more stable than its N3 counterpart: the ΔG_gas values vary in the range from 19.54 (5OH6СН₃U) to 83.14 (5NO₂6NH₂U) kJ/mol that is caused by a more effective delocalization of the excess charge through the uracil framework in the N1 anion. The hydration pronouncedly diminishes ΔG to the range from -0.02 (5OH6СН₃U) to 38.16 (5Br6NO₂U) kJ/mol due to the fact that the polar solvent is prone to stabilize more polar anionic states of uracils. Therefore, less polar uracil anions are more stable. We have defined the main factor influencing the N1/N3/О5/О6 distribution of anions, viz. the presence of the substituents in 5 and 6 positions of the pyrimidine ring. Herewith, the most favorable mechanism of the influence of 5-substituents has been previously defined as resonant whereas, as we found in this work, the inductive mechanism is more pronounced in the case of 6-substituents.

Molecular Modeling Studies of Some Uracil and New Deoxyuridine Derivatives

Molecular modeling results reported in this paper are crucial in highlighting the quantitative relationship between the optimized structure and computed molecular properties related to four newly synthesized uracil derivatives with promising biological potential as anticancer bioactive agents. Moreover, 5-fluorouracil (5-FU) and its tautomers and thiouracils molecular properties are studied and correlated with their biological activities. The great medical importance of these and similar molecular systems requires research on their quantitative structure-activity relationships (QSAR) in order to further improve our knowledge about how receptor binding, selectivity, and pharmacological effects are achieved. Modeling is performed in the ground and the first singlet excited states using density functional theory (DFT) and its time-dependent extension (TD-DFT), respectively.