Geometries of model chlorosilanes, R3SiCl, silanols, R3SiOH, and disiloxanes, (R3Si)2O, R = H, Me, as well as the thermochemistry of the reactions involving these species were modeled using 11 common density functionals in combination with five basis sets to examine the accuracy and applicability of various theoretical methods in organosilicon chemistry. As the model reactions, the proton affinities of silanols and siloxanes, hydrolysis of chlorosilanes and condensation of silanols to siloxanes were considered. As the reference values, experimental bonding parameters and reaction enthalpies were used wherever available. Where there are no experimental data, W1 and CBS-QB3 values were used instead. For the gas phase conditions, excellent agreement between theoretical CBS-QB3 and W1 and experimental thermochemical values was observed. All DFT methods also give acceptable values and the precision of various functionals used was comparable. No significant advantage of newer more advanced functionals over 'classical' B3LYP and PBEPBE ones was noted. The accuracy of the results was improved significantly when triple-zeta basis sets were used for energy calculations, instead of double-zeta ones. The accuracy of calculations for the reactions in water solution within the SCRF model was inferior compared to the gas phase. However, by careful estimation of corrections to the ΔHsolv and ΔGsolv of H(+) and HCl, reasonable values of thermodynamic quantities for the discussed reactions can be obtained.

The alkaline deacylation of a representative series of 1-(acylamino)alkylphosphonic acids [(AC)-AAP: (AC) = Ac, TFA, Bz; AAP = GlyP, AlaP, ValP, PglP and PheP] in an aqueous solution of KOH (2M) was investigated. The results suggested a two-stage reaction mechanism with a quick interaction of the hydroxyl ion on the carbonyl function of the amide R-C(O)-N(H)- group in the first stage, which leads to instant formation of the intermediary acyl-hydroxyl adducts of R-C(O−)2-N(H)-, visible in the 31P NMR spectra. In the second stage, these intermediates decompose slowly by splitting of the RC(O−)2-N(H)- function with the subsequent formation of 1-aminoalkylphosphonate and carboxylate ions.

5-Substituted 2-selenouridines (R5Se2U) are post-transcriptional modifications present in the first anticodon position of transfer RNA. Their functional role in the regulation of gene expression is elusive. Here, we present efficient syntheses of 5-methylaminomethyl-2-selenouridine (1, mnm5Se2U), 5-carboxymethylaminomethyl-2-selenouridine (2, cmnm5Se2U), and Se2U (3) alongside the crystal structure of the latter nucleoside. By using pH-dependent potentiometric titration, pKa values for the N3H groups of 1-3 were assessed to be significantly lower compared to their 2-thio-and 2-oxo-congeners. At physiological conditions (pH 7.4), Se2-uridines 1 and 2 preferentially adopted the zwitterionic form (ZI, ca. 90%), with the positive charge located at the amino alkyl side chain and the negative charge at the Se2-N3-O4 edge. As shown by density functional theory (DFT) calculations, this ZI form efficiently bound to guanine, forming the so-called "new wobble base pair", which was accepted by the ribosome architecture. These data suggest that the tRNA anticodons with wobble R5Se2Us may preferentially read the 5 -NNG-3 synonymous codons, unlike their 2-thio-and 2-oxo-precursors, which preferentially read the 5 -NNA-3 codons. Thus, the interplay between the levels of U-, S2U-and Se2U-tRNA may have a dominant role in the epitranscriptomic regulation of gene expression via reading of the synonymous 3 -A-and 3 -G-ending codons.

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The mechanisms of three selected identity substitution reactions at phosphorus and sulfur occurring with stereospecific inversion have been investigated using density functional theory (DFT). The first identity reaction between methoxyl anion and methyl ethylphenylphosphinate 1 reported in 1963 has been shown to proceed in a stepwise fashion according to the addition–elimination (A–E) mechanism involving formation of a pentacoordinate phosphorus intermediate (TBI-1). In contrast, the results of DFT studies of the identity chloride exchange reaction in (ethoxy)ethylphosphonochloridothionate 3 in acetone solution provided evidence that it proceeds synchronously according to the classical Ingold’s SN2-P mechanism. DFT calculations of the methoxyl–methoxy exchange reaction at sulfur in methyl p-toluenesulfinate 4 catalyzed by trifluoroacetic acid in methanol revealed that it proceeds stepwise (A–E mechanism), involving the formation of the high-coordinate sulfurane intermediate. In both identity transesterification reactions, 1 and 4, the transiently formed trigonal bipyramidal intermediates with the two methoxyl groups occupying apical positions (TBI-1 and TBI-4) have higher free energy barriers for the Berry-type pseudorotation than those for direct decomposition to starting phosphinate and sulfinate ensuring stereospecific inversion of configuration at the phosphinyl and sulfinyl centers. Thus, the DFT method proved its usefulness in the distinction between both mechanisms that are often indistinguishable by kinetic measurements.

Supramolecular motifs showing chemoresponsive properties toward organic molecules are sought after. Their selectivity, however, may depend even on a small structural change. Here, we demonstrate the influence of isomerization of glycoluril molecular clips, equipped with N-(4-methoxyphenyl)isonicotinamide sidewalls, on the complexation of resorcinol. Concentration-and temperature-dependent 1 H NMR and 1 H− 1 H ROESY NMR experiments along with theoretical studies were employed to determine the detailed mechanisms and thermodynamic parameters of complexation for both isomers with resorcinol. This study shows that clip 1, equipped with N-(4methoxyphenyl)isonicotinamide moieties oppositely directed along the glycoluril frame, is able to associate one resorcinol molecule within its cleft according to the "inner" mechanism with the equilibrium constant, K 283K = 2340 M −1 . Within the clip cleft, resorcinol forms hydrogen bonds via OH groups with oxygen atoms of clip's urea moieties and interacts with clip aromatic sidewalls via π−π stacking. Clip 2, the isomer whose N-(4-methoxyphenyl)isonicotinamide moieties are oriented in the same direction along the glycoluril core, possesses two binding sites and complexes resorcinol according to 1:2 stoichiometry. One of the binding sites is located in the clip cleft analogous to clip 1, whereas the second one is created by the mutual arrangement of pyridinyl moieties. The distance between nitrogen groups of individual pyridine moieties matches the distance of resorcinol hydroxyl groups facilitating the formation of two hydrogen bonds according to the "outer" mechanism. Both mechanisms are spontaneous (ΔG 11 and ΔG 12 < 0); however, the association constant differs, that is, K 11 = 2520 M −1 and K 12 = 650 M −1 at 283 K. Both mechanisms are exothermic; however, the "outer" mechanism is more sensitive to the increase of temperature, as ΔH 11 = −8.9 kcal/mol and ΔH 12 = −19.8 kcal/mol. Clip 2 is a first unique example of the glycoluril clip, which is able to complex two resorcinol molecules, as generally, glycoluril clips interact with dihydroxyaromatics according to 1:1 stoichiometry.

Geometrical cis- and trans- isomers of 2-chloro-, 2-bromo- and 2-fluoro-4-methyl-1,3,2-dioxaphosphorinan-2-thiones were obtained in a diastereoselective way by (a) sulfurization of corresponding cyclic PIII-halogenides, (b) reaction of cyclic phosphorothioic acids with phosphorus pentachloride and (c) halogen–halogen exchange at PIV-halogenide. Their conformation and configuration at the C4-ring carbon and phosphorus stereocentres were studied by NMR (1H, 31P) methods, X-ray analysis and density functional (DFT) calculations. The stereochemistry of displacement reactions (alkaline hydrolysis, methanolysis, aminolysis) at phosphorus and its mechanism were shown to depend on the nature of halogen. Cyclic cis- and trans-isomers of chlorides and bromides react with nucleophiles (HO−, CH3O−, Me2NH) with inversion of configuration at phosphorus. DFT calculations provided evidence that alkaline hydrolysis of cyclic thiophosphoryl chlorides proceeds according to the SN2-P mechanism with a single transition state according to the potential energy surface (PES) observed. The alkaline hydrolysis reaction of cis- and trans-fluorides afforded the same mixture of the corresponding cyclic thiophosphoric acids with the thermodynamically more stable major product. Similar DFT calculations revealed that substitution at phosphorus in fluorides proceeds stepwise according to the A–E mechanism with formation of a pentacoordinate intermediate since a PES with two transition states was observed.

The chloride-chloride exchange reaction in arenesulfonyl chlorides was investigated experimentally and theoretically by density functional theory (DFT) calculations. The second order rate constants and activation parameters of this identity reaction were determined for 22 variously substituted arenesulfonyl chlorides using radio-labeled Et4N36Cl. The chloride exchange rates of 11 sulfonyl chlorides bearing para-and meta-substituents (σ constants from −0.66 to +0.43) in the aromatic ring followed the Hammett equation with a ρ-value of +2.02. The mono- and di-ortho-alkyl substituted sulfonyl chlorides exhibit an enhanced reactivity although both inductive and steric effects lower the reaction rate. The DFT calculations of their structures together with X-ray data showed that an increased reactivity is mainly due to a peculiar, rigid, strongly compressed and sterically congested structure. The DFT studies of the title reaction revealed that it proceeds via a single transition state according to the SN2 mechanism. The analogous fluoride exchange reaction occurs according to the addition–elimination mechanism (A–E) and formation of a difluorosulfurandioxide intermediate. The reliability of the calculations performed was supported by the fact that the calculated relative rate constants and activation parameters correlate well with the experimental kinetic data.