Ab initio study on tautomerism of 2-thiouracil in the gas phase and in solution

Insights into Cisplatin Binding to Uracil and Thiouracils from IRMPD Spectroscopy and Tandem Mass Spectrometry

The monofunctional primary complexes cis-[PtCl(NH₃)₂(L)]⁺, formed by the reaction of cisplatin, a major chemotherapeutic agent, with four nucleobases L, i.e., uracil (U), 2-thiouracil (2SU), 4-thiouracil (4SU), and 2,4-dithiouracil (24dSU), have been studied by a combination of infrared multiple photon dissociation (IRMPD) action spectroscopy in both the fingerprint (900-1900 cm^-1) and the N-H/O-H stretching (3000-3800 cm^-1) ranges, energy-resolved collision-induced dissociation (CID) mass spectrometry, and density functional calculations at the B3LYP/LACVP/6-311G** level. On the basis of the comparison across the experimental features and the linear IR spectra of conceivable structures, the cisplatin residue is found to promote a monodentate interaction preferentially with the O4(S4) atoms of the canonical forms of U, 4SU, and 24dSU and to the S2 atom of 2SU, yielding the most stable structures. Additional absorptions reveal the presence of minor, alternative tautomers in the sampled ion populations of 2SU and 24dSU, underlying the ability of cisplatin to increase the prospect of (therapeutically beneficial) nucleic acid strand disorder. Implication of these evidence may provide insights into drug mechanism and design.

Radiation Induced One-Electron Oxidation of 2-Thiouracil in Aqueous Solutions

Oxidative damage to 2-thiouracil (2-TU) by hydroxyl (•OH) and azide (●N3) radicals produces various primary reactive intermediates. Their optical absorption spectra and kinetic characteristics were studied by pulse radiolysis with UV-vis spectrophotometric and conductivity detection and by time-dependent density functional theory (TD-DFT) method. The transient absorption spectra recorded in the reactions of •OH with 2-TU depend on the concentration of 2-TU, however, only slightly on pH. At low concentrations, they are characterized by a broad absorption band with a weakly pronounced maxima located at λ = 325, 340 and 385 nm, whereas for high concentrations, they are dominated by an absorption band with λmax ≈ 425 nm. Based on calculations using TD-DFT method, the transient absorption spectra at low concentration of 2-TU were assigned to the ●OH-adducts to the double bond at C5 and C6 carbon atoms (3●, 4●) and 2c-3e bonded ●OH adduct to sulfur atom (1…●OH) and at high concentration of 2-TU also to the dimeric 2c-3e S-S-bonded radical in neutral form (2●). The dimeric radical (2●) is formed in the reaction of thiyl-type radical (6●) with 2-TU and both radicals are in an equilibrium with Keq = 4.2 × 103 M-1. Similar equilibrium (with Keq = 4.3 × 103 M-1) was found for pH above the pKa of 2-TU which involves admittedly the same radical (6●) but with the dimeric 2c-3e S-S bonded radical in anionic form (2●-). In turn, ●N3-induced oxidation of 2-TU occurs via radical cation with maximum spin location on the sulfur atom which subsequently undergoes deprotonation at N1 atom leading again to thiyl-type radical (6●). This radical is a direct precursor of dimeric radical (2●).

The Role of Proton Transfer on Mutations

Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid-base characteristics of the nucleobases in Watson-Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs-DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.

Biomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNAMicrohelixes

The molecular structure of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil was analyzed under the effect of the first and second hydration shell by using the B3LYP density functional (DFT) method, and the results were compared to those obtained for the uracil molecule. A slight difference in the water distribution appears in these molecules. On the hydration of these molecules several trends in bond lengths and atomic charges were established. The ring in uracil molecule appears easier to be deformed and adapted to different environments as compared to that when it is thio-substituted. Molecular docking calculations of 2-thiouracil against three different pathogens: Bacillus subtilis, Escherichia coli and Candida albicans were carried out. Docking calculations of 2,4-dithiouracil ligand with various targeted proteins were also performed. Different DNA: RNA hybrid microhelixes with uridine, 2-thiouridine, 4-thiouridine and 2,4-dithiouridine nucleosides were optimized in a simple model with three nucleotide base pairs. Two main types of microhelixes were analyzed in detail depending on the intramolecular H-bond of the 2'-OH group. The weaker Watson-Crick (WC) base pair formed with thio-substituted uracil than with unsubstituted ones slightly deforms the helical and backbone parameters, especially with 2,4-dithiouridine. However, the thio-substitution significantly increases the dipole moment of the A-type microhelixes, as well as the rise and propeller twist parameters.

Effect of the sulfur atom on S2 and S4 positions of the uracil ring in different DNA:RNA hybrid microhelixes with three nucleotide base pairs

The effect of the sulphur atom on the uracil ring was analyzed in different DNA:RNA microhelixes with three nucleotide base-pairs, including uridine, 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, cytidine, adenosine and guanosine. Distinct backbone and helical parameters were optimized at different density functional (DFT) levels. The Watson-Crick pair with 2-thiouridine appears weaker than with uridine, but its interaction with water molecules appears easier. Two types of microhelixes were found, depending on the H-bond of H2' hydroxyl atom: A-type appears with the ribose ring in ³ E-envelope C_3' -endo, and B-type in ² E-envelope C_2' -endo. B-type is less common but it is more stable and with higher dipole-moment. The sulphur atoms significantly increase the dipole-moment of the microhelix, as well as the rise and propeller twist parameters. Simulations with four Na atoms H-bonded to the phosphate groups, and further hydration with explicit water molecules were carried out. A re-definition of the numerical value calculation of several base-pair and base-stacking parameters is suggested.

Internal conversion and intersystem crossing pathways in UV excited, isolated uracils and their implications in prebiotic chemistry

The photodynamic properties of molecules determine their ability to survive in harsh radiation environments. As such, the photostability of heterocyclic aromatic compounds to electromagnetic radiation is expected to have been one of the selection pressures influencing the prebiotic chemistry on early Earth. In the present study, the gas-phase photodynamics of uracil, 5-methyluracil (thymine) and 2-thiouracil-three heterocyclic compounds thought to be present during this era-are assessed in the context of their recently proposed intersystem crossing pathways that compete with internal conversion to the ground state. Specifically, time-resolved photoelectron spectroscopy measurements evidence femtosecond to picosecond timescales for relaxation of the singlet (1)ππ* and (1)nπ* states as well as for intersystem crossing to the triplet manifold. Trapping in the excited triplet state and intersystem crossing back to the ground state are investigated as potential factors contributing to the susceptibility of these molecules to ultraviolet photodamage.

C5-substituents of uridines and 2-thiouridines present at the wobble position of tRNA determine the formation of their keto-enol or zwitterionic forms - a factor important for accuracy of reading of guanosine at the 3΄-end of the mRNA codons

Modified nucleosides present in the wobble position of the tRNA anticodons regulate protein translation through tuning the reading of mRNA codons. Among 40 of such nucleosides, there are modified uridines containing either a sulfur atom at the C2 position and/or a substituent at the C5 position of the nucleobase ring. It is already evidenced that tRNAs with 2-thiouridines at the wobble position preferentially read NNA codons, while the reading mode of the NNG codons by R5U/R5S2U-containing anticodons is still elusive. For a series of 18 modified uridines and 2-thiouridines, we determined the pKa values and demonstrated that both modifying elements alter the electron density of the uracil ring and modulate the acidity of their N3H proton. In aqueous solutions at physiological pH the 2-thiouridines containing aminoalkyl C5-substituents are ionized in ca. 50%. The results, confirmed also by theoretical calculations, indicate that the preferential binding of the modified units bearing non-ionizable 5-substituents to guanosine in the NNG codons may obey the alternative C-G-like (Watson–Crick) mode, while binding of those bearing aminoalkyl C5-substituents (protonated under physiological conditions) and especially those with a sulfur atom at the C2 position, adopt a zwitterionic form and interact with guanosine via a ‘new wobble’ pattern.

Dihydropteridine/Pteridine as a 2H+/2e- Redox Mediator for the Reduction of CO2 to Methanol: A Computational Study

Conflicting experimental results for the electrocatalytic reduction of CO₂ to CH₃OH on a glassy carbon electrode by the 6,7-dimethyl-4-hydroxy-2-mercaptopteridine have been recently reported [ J. Am. Chem. Soc. 2014 , 136 , 14007 - 14010 , J. Am. Chem. Soc. 2016 , 138 , 1017 - 1021 ]. In this connection, we have used computational chemistry to examine the issue of this molecule's ability to act as a hydride donor to reduce CO₂. We first determined that the most thermodynamically stable tautomer of this aqueous compound is its oxothione form, termed here PTE. It is argued that this species electrochemically undergoes concerted 2H⁺/2e^- transfers to first form the kinetic product 5,8-dihydropteridine, followed by acid-catalyzed tautomerization to the thermodynamically more stable 7,8-dihydropteridine PTEH₂. While the overall conversion of CO₂ to CH₃OH by three successive hydride and proton transfers from this most stable tautomer is computed to be exergonic by 5.1 kcal/mol, we predict high activation free energies (ΔG^‡_HT) of 29.0 and 29.7 kcal/mol for the homogeneous reductions of CO₂ and its intermediary formic acid product by PTE/PTEH₂, respectively. These high barriers imply that PTE/PTEH₂ is unable, by this mechanism, to homogeneously reduce CO₂ on a time scale of hours at room temperature.

Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases

The trans-2-deoxyribosylation of 4-thiouracil (4SUra) and 2-thiouracil (2SUra), as well as 6-azauracil, 6-azathymine and 6-aza-2-thiothymine was studied using dG and E. coli purine nucleoside phosphorylase (PNP) for the in situ generation of 2-deoxy-α-D-ribofuranose-1-phosphate (dRib-1P) followed by its coupling with the bases catalyzed by either E. coli thymidine (TP) or uridine (UP) phosphorylases. 4SUra revealed satisfactory substrate activity for UP and, unexpectedly, complete inertness for TP; no formation of 2'-deoxy-2-thiouridine (2SUd) was observed under analogous reaction conditions in the presence of UP and TP. On the contrary, 2SU, 2SUd, 4STd and 2STd are good substrates for both UP and TP; moreover, 2SU, 4STd and 2'-deoxy-5-azacytidine (Decitabine) are substrates for PNP and the phosphorolysis of the latter is reversible. Condensation of 2SUra and 5-azacytosine with dRib-1P (Ba salt) catalyzed by the accordant UP and PNP in Tris∙HCl buffer gave 2SUd and 2'-deoxy-5-azacytidine in 27% and 15% yields, respectively. 6-Azauracil and 6-azathymine showed good substrate properties for both TP and UP, whereas only TP recognizes 2-thio-6-azathymine as a substrate. 5-Phenyl and 5-tert-butyl derivatives of 6-azauracil and its 2-thioxo derivative were tested as substrates for UP and TP, and only 5-phenyl- and 5-tert-butyl-6-azauracils displayed very low substrate activity. The role of structural peculiarities and electronic properties in the substrate recognition by E. coli nucleoside phosphorylases is discussed.

Conformations of 2-thiouracil in the aqueous solution and its adsorption behavior on the gold substrates explored by DFT calculations and experimental methods

2-Thiouracil, a thio-derivative of uracil, may appear in various tautomeric forms due to the different positions of protons. In this paper, the adsorption behavior and conformations of 2-thiouracil on the gold substrates are inspected by means of surface-enhanced Raman scattering (SERS) and density functional theory (DFT) calculations. The results indicate that all the enhanced bands are assigned to in-plane vibration modes. Besides, most of the bands related to N and S atoms are significantly enhanced and have obvious shifts in the SERS spectra. Furthermore, the CO stretching band at 1695 cm(-1) also appears in the SERS spectra. The theoretical SERS spectra of 2TU-Au₄ and 2TU2-Au₄ complexes agree well with the experimental SERS spectra of 2-thiouracil at 0.04 mM. Meanwhile, we calculate that the binding energies for 2TU2-Au₄ and 2TU-Au₄ are ca. 70 and 50 kcal/mol, respectively. Those results above imply that the 2TU and 2TU2 conformers can exist stably in the aqueous solution and both of them are vertically chemisorbed on the gold surfaces. For the 2TU, it is adsorbed on the gold surfaces through N1H position and the sulfur atom. While the 2TU2 adsorbed on the gold substrates through the N1 site and its deprotonated sulfur atom.

Oxidation reactions of 2-thiouracil: a theoretical and pulse radiolysis study

The reaction of hydroxyl radical ((•)OH) with the nucleic acid base analogue 2-thiouracil (1) has been studied by pulse radiolysis experiments and DFT. The generic intermediate radicals feasible for the (•)OH reactions with 1, namely, one electron oxidation product (1(•+)), (•)OH-adducts (3(•), 4(•), and 5(•)), and H-abstracted radicals (6(•) and 7(•)), were characterized by interpreting their electronic and structural properties along with calculated energetics and UV-vis spectra. Pulse radiolysis experiments showed that the transient formed in the reaction of (•)OH with 1 in water at pH 6.5 has λ(max) at 430 nm. A bimolecular rate constant, k(2) of 9.6 × 10(9) M(-1) s(-1), is determined for this reaction via competition kinetics with 2-propanol. The experiments suggested that the transient species could be a dimer radical cation 2(•+), formed by the reaction of 1 with the radical cation 1(•+). For this reaction, an equilibrium constant of 4.7 × 10(3) M(-1) was determined. The transient formed in the reaction of 1 with pulse radiolytically produced Br(2)(•-) at pH 6.5 as well as Cl(2)(•-) at pH 1 has also produced λ(max) at 430 nm and suggested the formation of 2(•+). The calculated UV-vis spectra of the transient species (1(•+), 3(•), 4(•), 5(•), 6(•), and 7(•)) showed no resemblance to the experimental spectra, while that of 2(•+) (λ(max) = 420 nm) agreed well with the experimental value and thus confirmed the formation of 2(•+). The 420 nm peak was due to σ → σ* electronic excitation centered on a 2-center-3-electron (2c-3e) sulfur-sulfur bond [-S∴S-]. 2(•+) is the first reported example of a dimer radical cation in a pyrimidine heterocyclic system. Further, 5-C and 6-C substituted (substituents are -F, -Cl, -NH(2), -N(CH(3))(2), -OCH(3), -CF(3), -CH(3), -CH(2)CH(3), n-propyl, phenyl, and benzyl) and 5,6-disubstituted 2-thiouracil systems have been characterized by DFT and found that the reaction (1 + 1(•+) → 2(•+)) is exergonic (1.12-13.63 kcal/mol) for many of them.

Here be dragons: docking and screening in an uncharted region of chemical space

To compare virtual and high-throughput screening in an unbiased way, 50,000 compounds were docked into the 3-dimensional structure of dihydrofolate reductase prospectively, and the results were compared to a subsequent experimental screening of the same library. Undertaking these calculations demanded careful database curation and control calculations with annotated inhibitors. These ultimately led to a ranked list of more likely and less likely inhibitors and to the prediction that relatively few inhibitors would be found in the empirical screen. The latter prediction turned out to be correct, with arguably no validated inhibitors found experimentally. Subsequent retesting of high-scoring docked molecules may have found 2 true inhibitors, although this remains uncertain due to experimental ambiguities. The implications of this study for screening campaigns are considered.

UV-Induced Generation of Rare Tautomers of 2-Thiouracils: A Matrix Isolation Study

Unimolecular photoisomerization reactions were studied for 2-thiouracil, 6-aza-2-thiothymine, 1-methyl-2-thiouracil, and 3-methyl-2-thiouracil isolated in low-temperature Ar matrixes. The IR spectra have revealed that before UV irradiation all the matrix-isolated compounds adopted exclusively the oxo-thione tautomeric form. Upon UV (lambda > 320 nm) irradiation of the matrixes, two oxo-thiol photoproducts were generated for monomeric 2-thiouracil as well as for monomeric 6-aza-2-thiothymine. Generation of these products corresponds to transfer of a proton from either the N(1)-H or N(3)-H group to the sulfur atom of the C(2)=S thiocarbonyl moiety. The first of the above reactions was photoreversible. As a consequence, after prolonged UV irradiation most of the material was transformed into the oxo-thiol-N(1)H form. The hydroxy-thiol tautomers of 2-thiouracil and 6-aza-2-thiothymine were also photogenerated as minor products. For 1-methyl-2-thiouracil and 3-methyl-2-thiouracil, thione --> thiol phototautomeric reactions yielded the oxo-thiol isomers of the compounds. Since these reactions were photoreversible, the final stages of the photoinduced processes corresponded, for both methylated 2-thiouracils, to photostationary states. All the products of the investigated photoreactions were identified by comparison of their IR spectra with the spectra calculated at the DFT(B3LYP)/6-311++G(2d,p) level.

2,4-Dithiouracil: the reproducible H-bonded structural motifs in the complexes with 18-membered crown ethers

2,4-dithiouracil (DTU) forms in the crystals the H-bonded monohydrates of a 1:1:1 ratio with 18-crown-6 (18C6) 1, cis,syn,cis-isomer of dicyclohexano-18-crown-6 (DCH6A) 2, and benzo-18-crown-6 (B18C6) 3, while the anhydrous adduct with cis,anti,cis-isomer of dicyclohexano-18-crown-6 (DCH6B) 4 is of a 2:1 ratio. In 1-3 the components reproducibly alternate in the chains, while in 4 the chains are built of the alternative centrosymmetric dimers of 2,4-dithiouracil and the molecules of the cis,anti,cis-isomer of dicyclohexano-18-crown-6.

Vibrational frequencies and structure of 2-thiouracil by Hartree-Fock, post-Hartree-Fock and density functional methods

Vibrational study of the biomolecule 2-thiouracil was carried out. Ab initio and density functional calculations were performed to assign the experimental spectra. A comparison with the uracil molecule was made, and specific scale factors were deduced and employed in the predicted frequencies of 2-thiouracil. Several scaling procedures were used. The geometry structure of the molecule was determined. The effect of sulfur substitution at C2 position in the uracil molecule, on the N1-H and N3-H frequencies and intensities reflects changes in proton donor abilities of these groups. Calculations with the 6-31 G** basis set with HF and DFT methods appear in general to be useful for interpretation of the general features of the IR and Raman spectra of the molecule. Using specific scale factors a very small error was obtained. The use of these specific scale factors resolve and correct some of the controversial assignments in the literature.

Quantum chemical studies on tautomerism of barbituric acid in gas phase and in solution

Ab inito and density functional theory (DFT) methods were used to study the tautomers of barbituric acid in the gas phase and in a polar medium. In the gas phase, the tautomers were optimized at the HF/6-31G*, MP2/6-31G* and B3LYP/6-31G*, B3PW91/6-31G* levels of theory. The self-consistent reaction field theory (SCRF) at the HF/6-31G* level of theory has been used to optimize the tautomers in a polar medium. The relative stability of the tautomers was compared in the gaseous and polar mediums. The ability of maximum hardness principle to predict the stable tautomer has been studied. The 13C-NMR chemical shift for carbon atoms in the tautomers was calculated and the results are discussed.