On the Mechanism of the Reactivity of 1,3-Dialkylimidazolium Salts under Basic to Acidic Conditions : A Combined Kinetic and Computational Study

Comprehensive spectroscopic kinetic studies illustrate an alternative mechanism for the traditional free-carbene intermediated H/D exchange reaction of 1,3-dialkylimidazolium salts under neutral (D2O) and acidic conditions (DCl/D2O 35wt% solution). The deuteration of high purity [bmim]Cl in D2O is studied at different temperatures, in absence of catalyst or impurities, to yield an activation energy. DFT transition-state modelling, of a small water cluster and [bmim] cation, also yields an activation energy which strongly supports the proposed mechanism. The presence of basic impurities are shown to significantly enhance the exchange reaction, which brings into question the need for further analysis of technical purities of ionic liquids and the implications for a wide range of chemical reactions in such media.Peer reviewe

A consistent model for the key complex in chronic beryllium disease

Abstract A hypothesis on the structure of the key complex in chronic beryllium disease (CBD) is discussed with respect to the current knowledge on CBD, and with respect to the constraints implied by the coordination chemistry of beryllium and experimental data on the engaged protein complexes. The structure hypothesis is based on the [Be4O]6+ moiety as a coordination center, which is also found in the so called “basic beryllium carboxylates”. The structure of a small molecular model, optimized at the DFT level of theory, is used to compare the structural demands of this coordination center with a structure of the in vitro model of a beryllium immunoprotein complex determined previously by protein crystallography (Clayton & al., Cell 2014, 158, 132). 9Be NMR chemical shielding values, quadrupole coupling constants and asymmetry parameters (η) have been calculated

A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations

International audienceMartini 3 is the new version of a widely used coarse-grained (CG) model that have been extensively parameterized to reproduce experimental and thermodynamic data. Based on a building-block approach, the new version shows a better coverage of the chemical space and more accurate predictions of interactions and molecular packing in general. Given these improvements, the Martini 3 model allows new applications such as studies involving protein–ligand interactions. In this chapter, a summary of the key elements of the new Martini version is presented, followed by an example of a practical application: a simulation of caffeine binding to the buried pocket of the adenosine A2A receptor, which is part of the GPCR family. Formulated as a hands-on tutorial, this chapter contains guidelines to build CG models of important systems, such as small drug-like molecules, transmembrane proteins, and lipid membranes. Finally, the last sections contain an outlook of possible future developments and notes describing useful information, limitations, and tips about Martini