Bioorthogonal masked acylating agents for proximity-dependent RNA labelling

RNA localization is highly regulated, with subcellular organization driving context-dependent cell physiology. Although proximity-based labelling technologies that use highly reactive radicals or carbenes provide a powerful method for unbiased mapping of protein organization within a cell, methods for unbiased RNA mapping are scarce and comparably less robust. Here we develop α-alkoxy thioenol and chloroenol esters that function as potent acylating agents upon controlled ester unmasking. We pair these probes with subcellular-localized expression of a bioorthogonal esterase to establish a platform for spatial analysis of RNA: bioorthogonal acylating agents for proximity labelling and sequencing (BAP-seq). We demonstrate that, by selectively unmasking the enol probe in a locale of interest, we can map RNA distribution in membrane-bound and membrane-less organelles. The controlled-release acylating agent chemistry and corresponding BAP-seq method expand the scope of proximity labelling technologies and provide a powerful approach to interrogate the cellular organization of RNAs.

Bond analysis in meta- and para-substituted thiophenols: overlap descriptors, local mode analysis, and QTAIM

CONTEXT

This study delves into the chemical nuances of thiophenols and their derivatives through a comprehensive computational analysis, moving beyond traditional energetic perspectives such as bond dissociation enthalpy and S-H dissociation dynamics. By employing the overlap model along with its topological descriptors (OP/TOP), quantum theory of atoms in molecules (QTAIM), and local vibrational mode (LVM) theories, the research provides a deeper understanding of the S-H and C-S bonding scenarios in substituted thiophenols. The investigation follows the electron-donating capacity of S-H substituent variation with the nature and positioning of other ring substituents. Energy profile analyses indicate distinct stability differences in the cis and trans conformations of meta- and para-PhSH systems, influenced by the electron-donating strength of these substituents. The study also uncovers significant variations in S-H bond distances and descriptor values, particularly in para-substituted PhSH, reflecting the influence of electron-donating or withdrawing substituents. In contrast, alterations at the meta-position show minimal effects on C-S bond descriptors, while para-substitutions markedly influence C-S bond characteristics, demonstrating a clear correlation with the electron-donating or withdrawing capabilities of the substituents. This research sheds light on the intricate bond dynamics in aromatic systems with diverse substituents, highlighting the complex interaction between electronic effects and molecular conformation.

METHODS

The study employs the ω B97X-D/Def2TZVP level of theory for molecular geometries, ensuring accurate characterization of structures as true minima via analytical harmonic frequency determination. The electronic properties of S-H and C-S bonds in variously substituted thiophenols were analyzed using OP/TOP, QTAIM, and LVM methodologies. Computational processes, including conformational scans, geometry optimizations, and vibrational frequency calculations, were conducted using Gaussian 09, with ultra-fine integration grids and tight convergence criteria for the SCF procedure. Bond descriptors were computed utilizing ChemBOS, Multiwfn, and LModeA software, providing a robust and detailed examination of bond properties.

The Mechanism of Metal-Containing Formate Dehydrogenases Revisited: The Formation of Bicarbonate as Product Intermediate Provides Evidence for an Oxygen Atom Transfer Mechanism

Mo/W-containing formate dehydrogenases (FDH) catalyzed the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active sites. While in the reaction of formate oxidation, the product is CO₂, which exits the active site via a hydrophobic channel; bicarbonate is formed as the first intermediate during the reaction at the active site. Other than what has been previously reported, bicarbonate is formed after an oxygen atom transfer reaction, transferring the oxygen from water to formate and a subsequent proton-coupled electron transfer or hydride transfer reaction involving the sulfido ligand as acceptor.

Acyl Group Migration in Pyranosides as Studied by Experimental and Computational Methods

Acyl group migration affects the synthesis, isolation, manipulation and purification of all acylated organic compounds containing free hydroxyl groups, in particular carbohydrates. While several isolated studies on the migration phenomenon in different buffers have been reported, comprehensive insights into the overall migration process in different monosaccharides under similar conditions have been lacking. Here, we have studied the acyl migration in different monosaccharides using five different acyl groups by a combination of experimental, kinetic and theoretical tools. The results show that the anomeric configuration in the monosaccharide has a major influence on the migration rate, together with the relative configurations of the other hydroxyl groups and the nature of the migrating acyl group. Full mechanistic model, based on computations, demonstrates that the acyl migration proceeds through an anionic stepwise mechanism with linear dependence on the [OH⁻] and the pK_a of the hydroxyl group toward which the acyl group is migrating.

Photochemical and Electrochemical Applications of Proton-Coupled Electron Transfer in Organic Synthesis

We present here a review of the photochemical and electrochemical applications of multi-site proton-coupled electron transfer (MS-PCET) in organic synthesis. MS-PCETs are redox mechanisms in which both an electron and a proton are exchanged together, often in a concerted elementary step. As such, MS-PCET can function as a non-classical mechanism for homolytic bond activation, providing opportunities to generate synthetically useful free radical intermediates directly from a wide variety of common organic functional groups. We present an introduction to MS-PCET and a practitioner's guide to reaction design, with an emphasis on the unique energetic and selectivity features that are characteristic of this reaction class. We then present chapters on oxidative N-H, O-H, S-H, and C-H bond homolysis methods, for the generation of the corresponding neutral radical species. Then, chapters for reductive PCET activations involving carbonyl, imine, other X═Y π-systems, and heteroarenes, where neutral ketyl, α-amino, and heteroarene-derived radicals can be generated. Finally, we present chapters on the applications of MS-PCET in asymmetric catalysis and in materials and device applications. Within each chapter, we subdivide by the functional group undergoing homolysis, and thereafter by the type of transformation being promoted. Methods published prior to the end of December 2020 are presented.

Probing the interactions between air bubbles and (bio)interfaces at the nanoscale using FluidFM technology

Understanding the molecular mechanisms underlying bubble-(bio)surfaces interactions is currently a challenge that if overcame, would allow to understand and control the various processes in which they are involved. Atomic force microscopy is a useful technique to measure such interactions, but it is limited by the large size and instability of the bubbles that it can use, attached either on cantilevers or on surfaces. We here present new developments where microsized and stable bubbles are produced using FluidFM technology, which combines AFM and microfluidics. The air bubbles produced were used to probe the interactions with hydrophobic samples, showing that bubbles in water behave like hydrophobic surfaces. They thus could be used to measure the hydrophobic properties of microorganisms' surfaces, but in this case the interactions are also influenced by electrostatic forces. Finally a strategy was developed to functionalize their surface, thereby modulating their interactions with microorganism interfaces. This new method provides a valuable tool to understand bubble-(bio)surfaces interactions but also to engineer them.

Super-resolved Optical Mapping of Reactive Sulfur-Vacancies in Two-Dimensional Transition Metal Dichalcogenides

Transition metal dichalcogenides (TMDs) represent a class of semiconducting two-dimensional (2D) materials with exciting properties. In particular, defects in 2D-TMDs and their molecular interactions with the environment can crucially affect their physical and chemical properties. However, mapping the spatial distribution and chemical reactivity of defects in liquid remains a challenge. Here, we demonstrate large area mapping of reactive sulfur-deficient defects in 2D-TMDs in aqueous solutions by coupling single-molecule localization microscopy with fluorescence labeling using thiol chemistry. Our method, reminiscent of PAINT strategies, relies on the specific binding of fluorescent probes hosting a thiol group to sulfur vacancies, allowing localization of the defects with an uncertainty down to 15 nm. Tuning the distance between the fluorophore and the docking thiol site allows us to control Föster resonance energy transfer (FRET) process and reveal grain boundaries and line defects due to the local irregular lattice structure. We further characterize the binding kinetics over a large range of pH conditions, evidencing the reversible adsorption of the thiol probes to the defects with a subsequent transitioning to irreversible binding in basic conditions. Our methodology provides a simple and fast alternative for large-scale mapping of nonradiative defects in 2D materials and can be used for in situ and spatially resolved monitoring of the interaction between chemical agents and defects in 2D materials that has general implications for defect engineering in aqueous condition.

Relationship between the Bulk and Surface Basicity of Aliphatic Amines: A Quantum Chemical Approach

To assess the surface basicity constant (pK _b) of aliphatic amine films, the use of a theoretical approach recently developed to evaluate the pK _a of carboxylic acid monolayers on the water surface is tested. The present paper gives a new full picture of the change of acid-base properties of surfactants during their aggregation at the air/water interface. The exploited approach is simple because it does not involve the construction of thermodynamic cycles but uses the Gibbs energies of the formation and dimerization of surfactant monomers in neutral and ionized forms in the aqueous and gaseous phases. The quantum chemical semiempirical PM3 method is applied to perform calculations using a conductor-like screening model, which takes into account the aqueous phase. The calculation shows that aliphatic amines, as well as carboxylic acids, are characterized by a change of the value of the basicity/acidity constant during the film formation. The film formation of surfactants leads to a decrease in their acid-base properties, i.e., the surface pK _a values of carboxylic acids and pK _b values of amines increase. However, unlike carboxylic acids, there is practically no dependence of the surface pK _b value on the alkyl chain length of the aliphatic amine, which is caused by almost identical contributions of one CH₂ fragment to the solvation Gibbs energy of neutral and ionized monomers within the calculation error. The obtained results agree with existing experimental data.

Synthesis of p-menthane-3,8-diol from citronellal over lignin-derived carbon acid catalysts

Sustainable carbon acid catalysts exhibited high-performance in the conversion of citronellal to p-menthane-3,8-diol via a carbocation-hydration pathway.

A mechanism of alkali metal carbonates catalysing the synthesis of β-hydroxyethyl sulfide with mercaptan and ethylene carbonate

The reaction of β-hydroxyethylation is essential to the current practice of organic chemistry. Here, we proposed a new and green route to synthesize 2-hydroxyethyl n-alkyl sulfide with n-alkyl mercaptan and ethylene carbonate (EC) in the presence of alkali carbonates as catalysts and revealed the mechanism by experiments and theoretical calculations. The reaction reported proceeds rapidly with high yields when it is performed at 120 °C and the catalytic loading is ∼1 mol%. This protocol is applicable to other mercaptans to synthesize the corresponding β-hydroxyethyl sulfide. Density functional theory-based calculations show the energy profile for the reaction pathway. The rate-determining step is the ring-opening of EC. A negatively charged O atom of alkali carbonates approaches the S atom of -SH under the influence of hydrogen bonds. An activated S atom that carries more negative charge serves as a nucleophilic reagent and assists in the ring-opening of EC by reducing the Mayer bond orders of the C1-O1 bond in EC. Alkali cations also contribute to the C1-O1 bond cleavage. The energy barrier for the ring-opening of EC decreases with the decrease of electronegativity of alkali cations. Subsequent transference of a H atom leads to the formation of β-hydroxyethyl sulfide, the dissociation of CO2 and the reduction of K2CO3.

Sulfhydryl-Directed Iridium-Catalyzed C-H/Diazo Coupling and Tandem Annulation of Naphthalene-1-thiols

The first sulfhydryl-directed iridium-catalyzed C-H/diazo coupling and tandem annulation of naphthalene-1-thiols has been developed. The framework of naphtho[1,8-bc]thiopyrans was constructed in a one-step reaction with good yields. This transformation provides a practical synthetic route for the widely used naphtho[1,8-bc]thiopyran derivatives.