The Aryne Phosphate Reaction

Pentaphosphorylation via the Anhydride of Dihydrogen Pentametaphosphate: Access to Nucleoside Hexa- and Heptaphosphates and Study of Their Interaction with Ribonuclease A

Pentametaphosphate is the little studied cyclic pentamer of the metaphosphate ion, [PO3]5 5-. We show that the doubly protonated form of this pentamer can be selectively dehydrated to provide the anhydride [P5O14]3- (1). This trianion is the well-defined condensed phosphate component of a novel reagent for attachment of a pentaphosphate chain to biomolecules all in one go. Here, we demonstrate by extending adenosine monophosphate (AMP) and uridine monophosphate (UMP) to their corresponding nucleoside hexaphosphates, while adenosine diphosphate (ADP) and uridine diphosphate (UDP) are phosphate chain-extended to the corresponding nucleoside heptaphosphates. Such constructs are of interest for their potential biological function with respect to RNA-processing enzymes. Thus, we go on to investigate in detail the interaction of the polyanionic constructs with ribonuclease A, a model protein containing a polycationic active site and for which X-ray crystal structures are relatively straightforward to obtain. This work presents a combined experimental and quantum chemical approach to understanding the interactions of RNase A with the new nucleoside hexa- and heptaphosphate constructs.

Synthesis and crystal structures of boryl ortho-silylaryl tri-fluoro-methane-sulfonates

We report the synthesis and structural characterization of three crystalline borylated ortho-silylaryl tri-fluoro-methane-sulfonates: 5-(4,4,5,5-tetra-methyl-1,3,2-dioxaborolan-2-yl)-2-(tri-methyl-sil-yl)phenyl tri-fluoro-methane-sulfonate, C16H24BF3O5SSi (1a), 4-(4,4,5,5-tetra-methyl-1,3,2-dioxaborolan-2-yl)-2-(tri-methyl-sil-yl)phenyl tri-fluoro-methane-sulfonate, C16H24BF3O5SSi (1b), and 2-methyl-4-(4,4,5,5-tetra-methyl-1,3,2-dioxaborolan-2-yl)-6-(tri-methyl-silyl)phen-yl tri-fluoro-methane-sulfonate, C17H26BF3O5SSi (2), which are versatile aryne precursors. For all three compounds, the heteroatom substituents are almost coplanar with the central aromatic moiety. C-heteroatom bonding metrics are unexceptional and fall withing the typical range of C-B, C-Si, and C-O single bonds. Despite numerous electronegative sites, only weak inter-molecular inter-actions are observed in the solid state.

On the aromaticity and stability of benzynes in the ground and lowest-lying triplet excited states

In this work, we have revisited the aromaticity of benzyne isomers at the unrestricted density functional theory level (UDFT) using the energetic, magnetic, and delocalization criteria. In addition, this last criterion has also been analyzed employing complete active space (CASSCF) calculations. The results show conservation of aromaticity in these monocycles. Additionally it is observed that this trend is maintained in polycyclic aromatic hydrocarbon derivatives such as biradical didehydrophenanthrenes. Do these results imply a violation of Baird's rule? The answer is No, because this conservation in aromaticity is due to the loss of hydrogen atoms affects only the electronic σ skeleton and exerts a minor influence on the π cloud. Additionally, we have analyzed the relative stability of benzyne isomers and their relationship with experimental ΔES-T values. According to the literature, the stability of the benzynes in the singlet state is due to an effective interaction between the electrons of the biradical centers; however, this effect is completely reversed in the triplet state, which explains why the para isomer has the lowest ΔES-T gap.

Development of 3-triazenylaryne and its application to iterative aryne reactions via o-triazenylarylboronic acids

Herein, a novel aryne species, 3-triazenylaryne, was developed and its regioselectivity was revealed. Based on the regioselectivity, various alkyne moieties were introduced by iodoalkynylation, and further derivatization to o-triazenylarylboronic acids as 3-alkynylaryne precursors was enabled. Therefore, 3-triazenylaryne was developed as a divergent platform for the generation of various 3-alkynylarynes.

Non-Hydrolysable Analogues of Cyclic and Branched Condensed Phosphates: Chemistry and Chemical Proteomics

Studies into the biology of condensed phosphates almost exclusively cover linear polyphosphates. However, there is evidence for the presence of cyclic polyphosphates (metaphosphates) in organisms and for enzymatic digestion of branched phosphates (ultraphosphates) with alkaline phosphatase. Further research of non-linear condensed phosphates in biology would profit from interactome data of such molecules, however, their stability in biological media is limited. Here we present syntheses of modified, non-hydrolysable analogues of cyclic and branched condensed phosphates, called meta- and ultraphosphonates, and their application in a chemical proteomics approach using yeast cell extracts. We identify putative interactors with overlapping hits for structurally related capture compounds underlining the quality of our results. The datasets serve as starting point to study the biological relevance and functions of meta- and ultraphosphates. In addition, we examine the reactivity of meta- and ultraphosphonates with implications for their "hydrolysable" analogues: Efforts to increase the ring-sizes of meta- or cyclic ultraphosphonates revealed a strong preference to form trimetaphosphate-analogue structures by cyclization and/or ring-contraction. Using carbodiimides for condensation, the so far inaccessible dianhydro product of ultraphosphonate, corresponding to P4 O11 2- , was selectively obtained and then ring-opened by different nucleophiles yielding modified cyclic ultraphosphonates.

Stabilized Molecular Diphosphorus Pentoxide, P2O5L2 (L = N-Donor Base), in the Synthesis of Condensed Phosphate-Organic Molecule Conjugates

Commercial phosphorus pentoxide reacts with some N-donor bases to give the adducts P₂O₅L₂ and P₄O₁₀L₃ (L = DABCO, pyridine, 4-tert-butylpyridine). The DABCO adducts were structurally characterized by single-crystal X-ray diffraction. It is proposed that P₂O₅L₂ and P₄O₁₀L₃ undergo interconversion through a "phosphate-walk" mechanism, which was evaluated using DFT calculations. P₂O₅(pyridine)₂ (1) efficiently transfers monomeric diphosphorus pentoxide to phosphorus oxyanion nucleophiles, yielding substituted trimetaphosphates and cyclo-phosphonate-diphosphates (P₃O₈R)^2- (R¹ = nucleosidyl, phosphoryl, alkyl, aryl, vinyl, alkynyl, H, F). Hydrolytic ring-opening of these compounds forms linear derivatives [R¹(PO₃)₂PO₃H]^3-, and nucleophilic ring-opening gives linear disubstituted [R¹(PO₃)₂PO₂R²]^3- compounds.

One-pot chemical pyro- and tri-phosphorylation of peptides by using diamidophosphate in water

Protein (pyro)phosphorylation is emerging as a post-translational modification (PTM) in signalling pathways involved in many cellular processes. However, access to synthetic pyrophosphopeptides that can serve as tools for understanding protein pyrophosphorylation is quite limited. Herein, we report a chemical phosphorylation method that enables the synthesis of pyrophosphopeptides in aqueous medium without the need for protecting groups. The strategy employs diamidophosphate (DAP) in a one-pot sequential phosphorylation-hydrolysis of mono-phosphorylated peptide precursors. This operationally simple method exploits the intrinsic nucleophilicity of a phosphate moiety installed on serine, threonine or tyrosine residues in complex peptides with excellent chemoselectivity and good yields under mild conditions. We demonstrate the installation of the pyrophosphate group within a wide range of model peptides and showcase the potential of this methodology by selectively pyrophosphorylating the highly functionalized Nopp140 peptide fragment. The potential to produce higher (poly)phosphorylated peptides was demonstrated as a proof-of-principle experiment where we synthesized the triphosphorylated peptides using this one-pot strategy.