"Upper" Ring Expansion of the Planar Blatter Radical via Photocyclization: Limitations and Impact on the Electronic Structure.

Photocyclization of 8-aryloxybenzo[e][1,2,4]triazines leads to the formation of π-expanded flat Blatter radicals for three phenanthryloxy and pyren-1-yloxy derivatives, whereas no photoreaction is observed for the perylen-3-yloxy precursor. Two of the new radicals are nonplanar, out of which one is unstable to isolation. The radical with the fused pyrene ring constitutes the largest thus far paramagnetic polycyclic π-system containing seven fused rings with 27 sp2-hybridized atoms and 29 π-delocalized electrons. The investigation of the reaction conditions demonstrated the higher efficiency of photoformation of the parent radical in polar solvents, which suggests a polar transition state and the S1 photoreactive state. The effect of π expansion on the electronic structure was investigated with spectroscopic (UV-vis, electron paramagnetic resonance) and electrochemical methods augmented with density functional theory computational studies. The molecular structure of one of the radicals was determined with a single-crystal X-ray diffraction method.

Tethered Blatter Radical for Molecular Grafting: Synthesis of 6-Hydroxyhexyloxy, Hydroxymethyl, and Bis(hydroxymethyl) Derivatives and Their Functionalization.

Synthetic access to 7-CF3-1,4-dihydrobenzo[e][1,2,4]triazin-4-yl radicals containing 4-(6-hydroxyhexyloxy)phenyl, 4-hydroxymethylphenyl or 3,5-bis(hydroxymethyl)phenyl groups at the C(3) position and their conversion to tosylates and phosphates are described. The tosylates were used to obtain disulfides and an azide with good yields. The Blatter radical containing the azido group underwent a copper(I)-catalyzed azide-alkyne cycloaddition with phenylacetylene under mild conditions, giving the [1,2,3]triazole product in 84% yield. This indicates the suitability of the azido derivative for grafting Blatter radical onto other molecular objects via the CuAAC "click" reaction. The presented derivatives are promising for accessing surfaces and macromolecules spin-labeled with the Blatter radical.

UV-photoelectron spectroscopy of stable radicals: the electronic structure of planar Blatter radicals as materials for organic electronics.

The electronic structure of Blatter radicals and a series of C(10)-substituted derivatives of 2-phenyl-3H-[1,2,4]triazino[5,6,1-kl]phenoxazin-3-yl (planar Blatter radicals) containing H, F, Cl, Br, CN, CF3 and OMe substituents was investigated by gas phase UV-photoelectron spectroscopy. The energy of the SOMO of the radicals, determined to be about 6.5 eV, was correlated with their electrochemical oxidation potentials, E0/+11/2, relative to the Fc/Fc+ couple in CH2Cl2 giving the correction of 6.60(1) eV. The optical band gap Eoptg ∼ 1.7 eV of the radicals yielded the electronic transport gap, Eelg, of about 2.1 eV, which is similar to the electronic parameters of pentacene. The radicals were analyzed by EPR spectroscopy and single crystal XRD methods, and all experimental data were compared to DFT computational results obtained at the CAM-B3LYP/6-311G(d,p) level of theory.

Ring-Fused 1,4-Dihydro[1,2,4]triazin-4-yls through Photocyclization.

Halogen lamp irradiation of benzo[e][1,2,4]triazines 2[X] in CH2Cl2 solutions leads to planar ring-fused 1,4-dihydro[1,2,4]triazin-4-yl radicals 1 through a novel, potentially general, cyclization mechanism. The scope and efficiency of the method were established for unsubstituted and ortho-substituted (X = NH2, Br, NO2) phenoxy, naphthyloxy, and quinolinoxy derivatives 2[X]. The regioselectivity of 2[X] photocyclization was rationalized with DFT computational methods. Radicals 1 were characterized by spectroscopic (UV-vis, EPR), electrochemical, and XRD methods.

Functional Planar Blatter Radical through Pschorr-Type Cyclization.

A series of functional 2-phenyl-3H-[1,2,4]triazino[5,6,1-kl]phenoxazin-3-yl (planar Blatter) radicals containing CO2Me, CN, and NO2 groups at the C(10) position and 2-phenyl-3H-pyrido[3,2-b][1,2,4]triazino[1,4]benzoxazin-3-yl have been obtained in yields of 40-80% by using the Pschorr-type cyclization and characterized by spectroscopic (ultraviolet-visible and electron paramagnetic resonance), electrochemical, and density functional theory methods. Two of these groups, CO2Me and NO2, have been transformed into CO2H and NH2, respectively, and conjugated with amino acids. One of the derivatives was analyzed by single-crystal X-ray diffraction methods.

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.

The influence of the C5 substituent on the 2-thiouridine desulfuration pathway and the conformational analysis of the resulting 4-pyrimidinone products.

In recent years, increasing attention has been focused on the posttranscriptional modifications present in transfer RNAs (tRNAs), which have been suggested to constitute another level of regulation of gene expression. The most representative among them are the 5-substituted 2-thiouridines (R5S2U), which are located in the wobble position of the anticodon and play a fundamental role in the tuning of the translation process. On the other hand, sulfur-containing biomolecules are the primary site for the attack of reactive oxygen species (ROS). We have previously demonstrated that under in vitro conditions that mimic oxidative stress in the cell, the S2U alone or bound to an RNA chain undergoes desulfuration to yield uridine and 4-pyrimidinone nucleoside (H2U) products. The reaction is pH- and concentration-dependent. In this study, for the first time, we demonstrate that the substituent at the C5 position of the 2-thiouracil ring of R5S2Us influences the desulfuration pathway, and thus the products ratio. As the substituent R changes, the amount of R5H2U increases in the order H->CH3O->CH3OC(O)CH2->HOC(O)CH2NHCH2-≈ CH3NHCH2-, and this effect is more pronounced at lower pH. The conformational analysis of the resulting R5H2U products indicates that independent of the nature of the R5 substituent, the R5H2U nucleosides predominantly adopt a C2'-endo sugar ring conformation, as opposed to the preferred C3'-endo conformation of the parent R5S2Us.

2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes.

2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon-anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3'-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif.

Transformation of a wobble 2-thiouridine to 2-selenouridine via S-geranyl-2-thiouridine as a possible cellular pathway.

The newly discovered S-geranylated 2-thiouridines (geS2U) (Dumelin et al., 2012) and 2-selenouridines (Se2U) were recently shown to be synthesized by a single enzyme (selenouridine synthase, SelU) through two distinct pathways using the same 2-thiouridine substrate (S2U); however, no clear catalytic mechanism was proposed. We suggest that S-geranyl-2-thiouridine is an intermediate of the SelU-catalyzed conversion of S2U to Se2U. The successful chemical transformation of S2U→geS2U→Se2U is demonstrated here as an initial approximation of the intracellular pathway. The structure of Se2U was confirmed by spectroscopic methods, which included, for the first time, (77)Se NMR data (δ 354ppm).

Desulfuration of 2-thiouridine with hydrogen peroxide in the physiological pH range 6.6-7.6 is pH-dependent and results in two distinct products.

The 2-thiomodified nucleosides, located at first position of tRNAs anticodon, may constitute a primary target for oxidative attack under conditions of oxidative stress. Desulfuration of 2-thiouridine (S2U) was investigated in the (1)H NMR scale in the presence of 100mM H2O2 and phosphate buffer in the physiological pH range, from pH 6.6 to 7.6. The obtained data demonstrate an intriguing result that within one unit of the pH range uridine is the major product of the S2U desulfuration in the pH 7.6, while the 4-pyrimidinone nucleoside (H2U) is dominant in pH 6.6. The possible desulfuration pathway and the biological importance of the transformation of S2U either to U or H2U are discussed in the context of the tRNA oxidative damage.