Synthesis of 4-Imidazolidinones from Diamides and Ethynyl Benziodoxolones via Double Michael-Type Addition: Ethynyl Benziodoxolones as Electrophilic Ynol Synthons.

The moiety of 4-imidazolidinone is an important structural motif in organic synthesis and medicinal chemistry. We present the synthesis of 4-imidazolidinones from various diamides with ethynyl benziodoxolones through double Michael-type addition, which is an unprecedented reaction mode for hypervalent alkynyl iodine compounds. cis-2,5-Disubstituted 4-imidazolidinones were diastereoselectively synthesized from amino acid derived diamides. Having derivatized the 4-imidazolidinones, several control experiments and density functional theory calculations were conducted to realize mechanistic insight.

Theoretical Study of the Mechanism of Ribosomal Peptide Bond Formation Using the ONIOM Method.

Peptide bond formation in living cells occurs at the peptidyl transferase center (PTC) of the large ribosomal subunit and involves the transfer of the peptidyl group from peptidyl-tRNA to aminoacyl-tRNA. Despite numerous kinetic and theoretical studies, many details of this reaction -such as whether it proceeds via a stepwise or concerted mechanism- remain unclear. In this study, we calculated the geometry and energy of the transition states and intermediates in peptide bond formation in the PTC environment using the ONIOM (our own n-layered integrated molecular orbital and molecular mechanics) method. The calculations indicated that the energy of the transition states of stepwise mechanisms are lower than those of concerted mechanisms and suggested that the reaction involves a neutral tetrahedral intermediate that is stabilized through the hydrogen-bonding network in the PTC environment. The results will lead to a better understanding of the mechanism of peptidyl transfer reaction, and resolve fundamental questions of the steps and molecular intermediates involved in peptide bond formation in the ribosome.

Enantioselective Protonation of Cyclic Carbonyl Ylides by Chiral Lewis Acid Assisted Alcohols.

Chiral Lewis acid-catalyzed asymmetric alcohol addition reactions to cyclic carbonyl ylides generated from N-(α-diazocarbonyl)-2-oxazolidinones featuring a dual catalytic system are reported. Construction of a chiral quaternary heteroatom-substituted carbon center was accomplished in which the unique heterobicycles were obtained in good yields with high stereoselection. The alcohol adducts were successfully converted to optically active oxazolidine-2,4-diones by hydrolysis. Mechanistic studies by DFT calculations revealed that alcohols could be activated by Lewis acids, enabling enantioselective protonation of the carbonyl ylides.

Methoxy Groups Increase Reactivity of Bifunctional Tetraarylphosphonium Salt Catalysts for Carbon Dioxide Fixation: A Mechanistic Study.

The development of carbon dioxide fixation under mild conditions is a central theme in organic synthesis. Despite the tremendous progress in the field of organocatalysis in the past two decades, the coupling reactions of epoxides with carbon dioxide that proceed at atmospheric pressure at temperatures of less than 100 °C have remained challenging. In our aspirational studies of tetraarylphosphonium salts (TAPS) catalysis, we report here the bifunctional TAPS-catalyzed synthesis of five-membered cyclic carbonates by chemical fixation using 1 atm of carbon dioxide at 60 °C. Intriguing substituent effects of TAPS were observed, in which electron-donating groups enhanced their reactivity. In addition, the mechanism was thoroughly investigated by undertaking both experimental and theoretical studies, suggesting that the electronic properties of TAPS affect carbon dioxide insertion into halohydrin intermediates. The results provided fruitful information to understand the origin of the TAPS behavior, which would contribute to the design of novel catalysts for carbon dioxide capture.

Amine-Urea-Mediated Asymmetric Cycloadditions between Nitrile Oxides and o-Hydroxystyrenes by Dual Activation.

The first example of asymmetric 1,3-dipolar cycloadditions between nitrile oxides and o-hydroxystyrenes, mediated by cinchona-alkaloid-based amine-ureas is reported. The method is based on a dual activation involving both LUMO and HOMO activations. In addition to the stoichiometric asymmetric induction, a catalytic amount of amine-urea enables the cycloadditions to proceed in an enantioselective manner. Computational studies strongly support the HOMO activation of o-hydroxystyrenes and LUMO activation of nitrile oxides by hydrogen-bonding interactions with the Brønsted acid/base bifunctional catalyst.

Enzymatic and structural characterization of an archaeal thiamin phosphate synthase.

Studies on thiamin biosynthesis have so far been achieved in eubacteria, yeast and plants, in which the thiamin structure is formed as thiamin phosphate from a thiazole and a pyrimidine moiety. This condensation reaction is catalyzed by thiamin phosphate synthase, which is encoded by the thiE gene or its orthologs. On the other hand, most archaea do not seem to have the thiE gene, but instead their thiD gene, coding for a 2-methyl-4-amino-5-hydroxymethylpyrimidine (HMP) kinase/HMP phosphate kinase, possesses an additional C-terminal domain designated thiN. These two proteins, ThiE and ThiN, do not share sequence similarity. In this study, using recombinant protein from the hyperthermophile archaea Pyrobaculum calidifontis, we demonstrated that the ThiN protein is an analog of the ThiE protein, catalyzing the formation of thiamin phosphate with the release of inorganic pyrophosphate from HMP pyrophosphate and 4-methyl-5-ß-hydroxyethylthiazole phosphate (HET-P). In addition, we found that the ThiN protein can liberate an inorganic pyrophosphate from HMP pyrophosphate in the absence of HET-P. A structure model of the enzyme-product complex of P. calidifontis ThiN domain was proposed on the basis of the known three-dimensional structure of the ortholog of Pyrococcus furiosus. The significance of Arg320 and His341 residues for thiN-coded thiamin phosphate synthase activity was confirmed by site-directed mutagenesis. This is the first report of the experimental analysis of an archaeal thiamin synthesis enzyme.

Facilitated recruitment of Pdc2p, a yeast transcriptional activator, in response to thiamin starvation.

In Saccharomyces cerevisiae, genes involved in thiamin pyrophosphate (TPP) synthesis (THI genes) and the pyruvate decarboxylase structural gene PDC5 are transcriptionally induced in response to thiamin starvation. Three positive regulatory factors (Thi2p, Thi3p, and Pdc2p) are involved in the expression of THI genes, whereas only Pdc2p is required for the expression of PDC5. Thi2p and Pdc2p serve as transcriptional activators and each factor can interact with Thi3p. The target consensus DNA sequence of Thi2p has been deduced. When TPP is not bound to Thi3p, the interactions between the regulatory factors are increased and THI gene expression is upregulated. In this study, we demonstrated that Pdc2p interacts with the upstream region of THI genes and PDC5. The association of Pdc2p or Thi2p with THI gene promoters was enhanced by thiamin starvation, suggesting that Pdc2p and Thi2p assist each other in their recruitment to the THI promoters via interaction with Thi3p. It is highly likely that, under thiamin-deprived conditions, a ternary Thi2p/Thi3p/Pdc2p complex is formed and transactivates THI genes in yeast cells. On the other hand, the association of Pdc2p with PDC5 was unaffected by thiamin. We also identified a DNA element in the upstream region of PDC5, which can bind to Pdc2p and is required for the expression of PDC5.

Facile and convenient method of deuterium gas generation using a Pd/C-catalyzed H2-D2 exchange reaction and its application to synthesis of deuterium-labeled compounds.

The Pd/C-catalyzed H(2)-D(2) exchange reaction using a H(2)-D(2)O combination provided a general, efficient and environmentally friendly route for the preparation of deuterium gas (D(2)). H(2) sealed in a reaction flask was converted into nearly pure D(2), which could be used for the Pd/C-catalyzed one-pot reductive deuteration of various reducible functionalities and the chemoselective one-pot deuterogenation of olefin and acetylene. Additionally, we established the capturing method of the generated D(2) in a balloon, which was successfully applied to the Pd/C-catalyzed reductive mono-N-alkylation of a primary amine using nitrile as the alkylating reagent.

Efficient h/d exchange reactions of alkyl-substituted benzene derivatives by means of the Pd/C-H(2)-D(2)O system.

A method for efficient and extensive H/D exchange of substituted benzene derivatives which is catalyzed by heterogeneous Pd/C in D(2)O as a deuterium source under hydrogen atmosphere is described. Multi-deuterium incorporation into unactivated linear or branched alkyl chains that bear a carboxyl, hydroxyl, ether, ester, or amide moiety and are connected with a benzene ring was achieved by using the Pd/C-H(2)-D(2)O system. The present method does not require expensive deuterium gas or any special equipment.

Novel Pd/C-catalyzed redox reactions between aliphatic secondary alcohols and ketones under hydrogenation conditions: application to H-D exchange reaction and the mechanistic study.

A liquid-phase redox system between secondary alcohols and ketones is described. Deuteration of either secondary alcohols or ketones using the Pd/C-H2-D2O system gave a mixture of deuterium-labeled secondary alcohols and ketones. The results indicated that the secondary alcohol was oxidized to the corresponding ketone without oxidants under the hydrogenation conditions and the hydrogenation of the aliphatic ketone to the corresponding secondary alcohol simultaneously proceeded. Detailed mechanistic studies on the redox system as well as the H-D exchange reaction are discussed.

Complete replacement of H2 by D2 via Pd/C-catalyzed H/D exchange reaction.

[reaction: see text] A general and in situ D2 gas generation method using 10% Pd/C-catalyzed H2-D2 exchange reaction in a H2-D2O system has been developed. H2 gas sealed in a reaction flask was efficiently converted into nearly pure D2 gas, which can be used for the reductive deuteration of substrates possessing reducible functionalities within the molecule.

Efficient C-H/C-D exchange reaction on the alkyl side chain of aromatic compounds using heterogeneous Pd/C in D2O.

[reaction: see text] An efficient and extensive deuterium incorporation using heterogeneous Pd/C-D(2)O-H(2) system into many different types of unactivated C-H bond positions was developed. The present method provides a deuterium gas-free, totally catalytic, and post-synthetic deuterium labeling method in D(2)O media.

Palladium-catalyzed H-D exchange into nucleic acids in deuterium oxide.

We have developed an efficient and extensive deuterium incorporation method using a heterogeneous Pd/C-D2O-H2 system into the base moiety of nucleic acids. The results presented here provide a deuterium gas-free, totally catalytic and post-synthetic deuterium labeling method in D2O media.