Intramolecular C-glycosylation of 2-O-benzylated pentenyl mannopyranosides: remarkable 1,2-trans stereoselectivity

The IDCP-promoted intramolecular C-glycosylation of pentenyl α-mannopyranosides carrying, at O-2, an activated benzyl group gave, unexpectedly, the 1,2-trans-fused bicyclic product which corresponds to an α-C-aryl mannopyranose derivative. This remarkable, strained C-glycosyl compound was rapidly epimerized to the more stable 1,2-cis product on treatment with BF₃·Et₂O. The IDCP-reaction product could be elaborated into a 2-(α-C-mannopyranosyl)-3,4,5-trimethoxybenzyl alcohol derivative.     

Effects of DNA secondary structure on oligonucleotide probe binding efficiency

Secondary structure motifs in nucleic acid probes generally impair intended hybridization reactions and so efforts to predict and avoid such structures are commonly employed in probe design schemes. Another key facet of probe design that has received much less attention, however, is that secondary structure at targeted probe binding site regions may also impair hybridization. Thus, evaluation of both probe and target site secondary structures together should improve hybridization prediction and design effectiveness. Several challenges confound this goal, including imperfect empirical rules and parameters underlying predictions and the fact that folding algorithms scale poorly with respect to sequence length. Here, we attempt to quantify the consequences of target site structure on predicted hybridization using sequences sampled from the human genome. We also provide a methodology for choosing a reasonable “window size” around target sites that is as small as possible without compromising folding algorithm prediction accuracy.     

Reactivity of monolayer-protected gold nanoclusters at dye-sensitized liquid/liquid interfaces

Hexanethiolate monolayer-protected gold nanoclusters (MPCs) were used as redox quenchers at the polarizable water/1,2-dichloroethane (DCE) interface. Photocurrent responses originating from the heterogeneous quenching of photoexcited water soluble porphyrin complexes by MPCs dissolved in the DCE phase were observed. As MPCs can function as both electron acceptors and donors, the photocurrent results from the superposition of two simultaneous processes, which correspond to the oxidation and reduction of MPCs. The magnitude of the net photocurrent is essentially determined by the balance of the kinetics of these two processes, which can be controlled by tuning the Galvani potential difference between the two phases. We show that, within the available potential window, the apparent electron-transfer rate constants follow classical Butler-Volmer dependence on the applied potential difference.     

Artificial metalloenzymes for enantioselective catalysis based on biotin-avidin

Homogeneous and enzymatic catalysis offer complementary means to generate enantiomerically pure compounds. Incorporation of achiral biotinylated rhodium-diphosphine complexes into (strept)avidin yields artificial metalloenzymes for the hydrogenation of N-protected dehydroamino acids. A chemogenetic optimization procedure allows one to produce (R)-acetamidoalanine with 96% enantioselectivity. These hybrid catalysts display features reminiscent both of enzymatic and of homogeneous systems.     

Artificial metalloenzymes: (strept)avidin as host for enantioselective hydrogenation by achiral biotinylated rhodium-diphosphine complexes

We report on the generation of artificial metalloenzymes based on the noncovalent incorporation of biotinylated rhodium-diphosphine complexes in (strept)avidin as host proteins. A chemogenetic optimization procedure allows one to optimize the enantioselectivity for the reduction of acetamidoacrylic acid (up to 96% ee (R) in streptavidin S112G and up to 80% ee (S) in WT avidin). The association constant between a prototypical cationic biotinylated rhodium-diphosphine catalyst precursor and the host proteins was determined at neutral pH: log K(a) = 7.7 for avidin (pI = 10.4) and log K(a) = 7.1 for streptavidin (pI = 6.4). It is shown that the optimal operating conditions for the enantioselective reduction are 5 bar at 30 degrees C with a 1% catalyst loading.     

Elicitor-Induced VOC Emission by Grapevine Leaves: Characterisation in the Vineyard

The present study is aimed at determining whether leaf volatile organic compounds (VOCs) are good markers of the grapevine response to defence elicitors in the field. It was carried out in two distinct French vineyards (Burgundy and Bordeaux) over 3 years. The commercial elicitor Bastid^® (Syngenta, Saint-Sauveur, France) (COS-OGA) was first used to optimise the VOCs’ capture in the field; by bagging stems together with a stir bar sorptive extraction (SBSE) sensor. Three elicitors (Bastid^®, copper sulphate and methyl jasmonate) were assessed at three phenological stages of the grapevines by monitoring stilbene phytoalexins and VOCs. Stilbene production was low and variable between treatments and phenological stages. VOCs—particularly terpenes—were induced by all elicitors. However, the response profiles depended on the type of elicitor, the phenological stage and the vineyard, and no sole common VOC was found. The levels of VOC emissions discriminated between weak (Bastid^® and copper sulphate) and strong (methyl jasmonate) inducers. Ocimene isomers were constitutively present in the overall blends of the vineyards and increased by the elicitors’ treatments, whilst other VOCs were newly released throughout the growing seasons. Nonetheless, the plant development and climate factors undoubtedly influenced the release and profiles of the leaf VOCs.     

Collective Effects in Ionic Liquid [emim][Tf2N] and Ionic Paramagnetic Nitrate Solutions without Long-Range Structuring

Mesoscopic shear elasticity has been revealed in ordinary liquids both experimentally by reinforcing the liquid/surface interfacial energy and theoretically by nonextensive models. The elastic effects are here examined in the frame of small molecules with strong electrostatic interactions such as room temperature ionic liquids [emim][Tf2N] and nitrate solutions exhibiting paramagnetic properties. We first show that these charged fluids also exhibit a nonzero low-frequency shear elasticity at the submillimeter scale, highlighting their resistance to shear stress. A neutron scattering study completes the dynamic mechanical analysis of the paramagnetic nitrate solution, evidencing that the magnetic properties do not induce the formation of a structure in the solution. We conclude that the elastic correlations contained in liquids usually considered as viscous away from any phase transition contribute in an effective way to collective effects under external stress whether mechanical or magnetic fields.     

Torsionally broken symmetry assists infrared excitation of biomimetic charge-coupled nuclear motions in the electronic ground state

The concerted interplay between reactive nuclear and electronic motions in molecules actuates chemistry. Here, we demonstrate that out-of-plane torsional deformation and vibrational excitation of stretching motions in the electronic ground state modulate the charge-density distribution in a donor-bridge-acceptor molecule in solution. The vibrationally-induced change, visualised by transient absorption spectroscopy with a mid-infrared pump and a visible probe, is mechanistically resolved by ab initio molecular dynamics simulations. Mapping the potential energy landscape attributes the observed charge-coupled coherent nuclear motions to the population of the initial segment of a double-bond isomerization channel, also seen in biological molecules. Our results illustrate the pivotal role of pre-twisted molecular geometries in enhancing the transfer of vibrational energy to specific molecular modes, prior to thermal redistribution. This motivates the search for synthetic strategies towards achieving potentially new infrared-mediated chemistry.

Channelling vibrational excitation energy to achieve ground-state charge-transfer (CT)-assisted isomerization in a donor-bridge-acceptor molecule in solution.     

Periodic Mesoporous Organosilica Nanoparticles for CO2 Adsorption at Standard Temperature and Pressure

(1) Background: Due to human activities, greenhouse gas (GHG) concentrations in the atmosphere are constantly rising, causing the greenhouse effect. Among GHGs, carbon dioxide (CO₂) is responsible for about two-thirds of the total energy imbalance which is the origin of the increase in the Earth’s temperature. (2) Methods: In this field, we describe the development of periodic mesoporous organosilica nanoparticles (PMO NPs) used to capture and store CO₂ present in the atmosphere. Several types of PMO NP (bis(triethoxysilyl)ethane (BTEE) as matrix, co-condensed with trialkoxysilylated aminopyridine (py) and trialkoxysilylated bipyridine (Etbipy and iPrbipy)) were synthesized by means of the sol-gel procedure, then characterized with different techniques (DLS, TEM, FTIR, BET). A systematic evaluation of CO₂ adsorption was carried out at 298 K and 273 K, at low pressure. (3) Results: The best values of CO₂ adsorption were obtained with 6% bipyridine: 1.045 mmol·g⁻¹ at 298 K and 2.26 mmol·g⁻¹ at 273 K. (4) Conclusions: The synthetized BTEE/aminopyridine or bipyridine PMO NPs showed significant results and could be promising for carbon capture and storage (CCS) application.     

Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies

Monoclonal antibodies are emerging as a viable treatment for the coronavirus disease 19 (COVID-19). However, newly evolved variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can reduce the efficacy of currently available antibodies and can diminish vaccine-induced immunity. Here, we demonstrate that the microscopic dynamics of neutralizing monoclonal antibodies can be profoundly modified by the mutations present in the spike proteins of the SARS-COV-2 variants currently circulating in the world population. The dynamical perturbations within the antibody structure, which alter the thermodynamics of antigen recognition, are diverse and can depend both on the nature of the antibody and on the spatial location of the spike mutation. The correlation between the motion of the antibody and that of the spike receptor binding domain (RBD) can also be changed, modulating binding affinity. Using protein-graph-connectivity networks, we delineated the mutant-induced modifications in the information-flow along allosteric pathway throughout the antibody. Changes in the collective dynamics were spatially distributed both locally and across long-range distances within the antibody. On the receptor side, we identified an anchor-like structural element that prevents the detachment of the antibodies; individual mutations there can significantly affect the antibody binding propensity. Our study provides insight into how virus neutralization by monoclonal antibodies can be impacted by local mutations in the epitope via a change in dynamics. This realization adds a new layer of sophistication to the efforts for rational design of monoclonal antibodies against new variants of SARS-CoV2, taking the allostery in the antibody into consideration.

Mutations in the new variants of SARS-CoV-2 spike protein modulates the dynamics of the neutralizing antibodies. Capturing such modulations from MD simulations and graph network model identifies the role of mutations in facilitating immune evasion.