The halolactonization reaction is one of the most common electrophilic addition reactions to alkenes. The mechanism is generally viewed as a two-step pathway, which involves the formation of an ionic intermediate, in most cases a haliranium ion. Recently, an alternative concerted mechanism was proposed, in which the nucleophile of the reaction played a key role in the rate determining step by forming a pre-polarized complex with the alkene. This pathway was coined the nucleophile-assisted alkene activation (NAAA) mechanism. Metadynamics simulations on a series of model halolactonization reactions were used to obtain the full dynamic trajectory from reactant to product and investigate the explicit role of the halogen source and solvent molecules in the mechanism. The results in this work ratify the occasional preference of a concerted mechanism over the classic two-step transformation under specific reaction conditions. Nevertheless, as the stability of both the generated substrate cation and counter-anion increase, a transition towards the classic two-step mechanism was observed. NCI analyses on the transition states revealed that the activating role of the nucleophile is independent of the formation and stability of the intermediate. Additionally, the dynamic insights obtained from the metadynamics simulations and NCI analyses employed in this work, unveiled the presence of -directing noncovalent interactions, such as hydrogen bonding, between the alkenoic acid and the halogen source, which rationalized the experimentally observed diastereoselectivities. Explicit noncovalent interactions between the reactants and a protic solvent or basic additive are able to disrupt these -directing noncovalent interactions, affecting the diastereoselective outcome of the reaction.
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http://dx.doi.org/10.1039/d1sc01014j | DOI Listing |
PLoS One
January 2025
Manchester Cancer Research Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.
Non-covalent protein-protein interactions are one of the most fundamental building blocks in cellular signalling pathways. Despite this, they have been historically hard to identify using conventional methods due to their often weak and transient nature. Using genetic code expansion and incorporation of commercially available unnatural amino acids, we have developed a highly accessible method whereby interactions between biotinylated ubiquitin-like protein (UBL) probes and their binding partners can be stabilised using ultraviolet (UV) light-induced crosslinks.
View Article and Find Full Text PDFJ Mol Model
January 2025
Applied Nuclear Technology in Geosciences Key Laboratory of Sichuan Province, Chengdu University of Technology, Chengdu, People's Republic of China.
Context: The study of the influence of solvent on 1-bromo adamantane (BAD) exposes prominent solvatochromatic shifts in the optical absorbance and substantial solvent effects on the electronic structure. This facilitates the molecular probe abilities for the BAD with respect to the surrounding environments such as dielectric constant and polarity. BAD exhibits positive solvatochromism for nonpolar solvents and negative solvatochromatic shifts for polar and aromatic solvents.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
The Effective Fragment Potential (EFP) method, a polarizable quantum mechanics-based force field for describing non-covalent interactions, is utilized to calculate protein-ligand interactions in seven inactive cyclin-dependent kinase 2-ligand complexes, employing structural data from molecular dynamics simulations to assess dynamic and solvent effects. Our results reveal high correlations between experimental binding affinities and EFP interaction energies across all the structural data considered. Using representative structures found by clustering analysis and excluding water molecules yields the highest correlation (R2 of 0.
View Article and Find Full Text PDFACS Phys Chem Au
January 2025
Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo, São José dos Campos, 12247-014 São Paulo, Brazil.
The unique properties and versatile applications of natural deep eutectic solvents (NaDES) have sparked significant interest in the field of green chemistry. Comprised of natural components that form liquids at room temperature through strong noncovalent electrostatic interaction, these solvents are cost-effective, nontoxic, and versatile. Betaine chloride-based NaDES, in particular, have shown promise in biocatalysis and sugar extraction due to their excellent properties.
View Article and Find Full Text PDFRSC Adv
January 2025
Dipartimento di Scienze e Innovazione Tecnologica, Università Del Piemonte Orientale A. Avogadro Viale T. Michel 11 15121 Alessandria Italy
A novel synthesis of a nanometric MCM-41 from biogenic silica obtained from rice husk is here presented. CTABr and Pluronic F127 surfactants were employed as templating agents to promote the formation of a long-range ordered 2D-hexagonal structure with cylindrical pores and to limit the particle growth at the nanoscale level thus resulting in a material with uniform particle size of 20-30 nm. The physico-chemical properties of this sample (RH-nanoMCM) were investigated through a multi-technique approach, including PXRD, Si MAS NMR, TEM, -potential and N physisorption analysis at 77 K.
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