Quantum chemical study of the properties of grignard reagents

http://www.ester.ee/record=b1566122~S1*es

Proton and Lithium Cation Binding to Some β-Dicarbonyl Compounds. A Theoretical Study

DFT B3LYP/6-311+G** calculations were performed to study the proton and lithium cation binding to the acetylacetone, hexafluoroacetylacetone, diacetamide, and hexafluorodiacetamide. It was shown that the most stable Li+ adduct always corresponds to cyclic complex based on the trans, trans-keto form of the base. The product of protonation was found to be similar trans, trans-keto form based cyclic structure in case of diacetamide and hexafluorodiacetamide, while for acetylacetone and hexafluoroacetylacetone the protonation simply involves the addition of proton to (free) carbonyl oxygen in already cyclic enol form of the base with possible rotation of O−H bond

Molecular Dynamics Simulations of the Interactions between Glial Cell Line-Derived Neurotrophic Factor Family Receptor GFR alpha 1 and Small-Molecule Ligands

The glial cell line-derived neurotrophic factor (GDNF) family ligands (GFLs) support the survival and functioning of various neuronal populations. Thus, they could be attractive therapeutic agents against a multitude of neurodegenerative diseases caused by progressive death of GFLs responsive neurons. Small-molecule ligands BT13 and BT18 show an effect on GDNF family receptor GFR alpha 1 and RET receptor tyrosine kinase RetA function. Thus, their potential binding sites and interactions were explored in the GDNF-GFR alpha 1-RetA complex using molecular docking calculations as well as molecular dynamics (MD) simulations. Three possible regions were examined: the interface between GDNF and GFR alpha 1 (region A), the RetA interface with GFR alpha 1 (region B), and a possible allosteric site in GFR alpha 1 (region C). The results obtained by the docking calculations and the MD simulations indicate that the preferable binding occurs at the allosteric site. A less preferable binding site was detected on the RetA surface interfacing GFR alpha 1. In the membrane-bound state of RetA this can enable compounds BT13 and BT18 to act as direct RetA agonists. The analysis of the MD simulations shows hydrogen bonds for BT13 and significant hydrophobic interactions with GFR alpha 1 for BT13 and BT18 at the allosteric site.Peer reviewe

Small-Molecule Ligands as Potential GDNF Family Receptor Agonists

To find out potential GDNF family receptor alpha 1 (GFR alpha 1) agonists, small molecules were built up by molecular fragments according to the structure-based drug design approach. Molecular docking was used to identify their binding modes to the biological target GFRa1 in GDNF-binding pocket. Thereafter, commercially available compounds based on the best predicted structures were searched from ZINC and MolPort databases (similarity >= 80%). Five compounds from the ZINC library were tested in phosphorylation and luciferase assays to study their ability to activate GFR alpha 1-RET. A bidental compound with two carboxyl groups showed the highest activity in molecular modeling and biological studies. However, the relative position of these groups was important. The meta-substituted structure otherwise identical to the most active compound 2-[4-(5-carboxy-1H-1,3-benzodiazol-2-yl) phenyl]-1H-1,3-benzodiazole-5-carboxylic acid was inactive. A weaker activity was detected for a compound with a single carboxyl group, that is, 4-(1,3-benzoxazol-2-yl) benzoic acid. The substitution of the carboxyl group by the amino or acetamido group also led to the loss of the activity.Peer reviewe

Computational Study of Copper-Free Sonogashira Cross-Coupling Reaction

The copper-free Sonogashira cross-coupling reaction consisting of oxidative addition, <i>cis–trans</i> isomerization, deprotonation, and reductive elimination was computationally modeled using the DFT B97D/cc-pVDZ method for reaction between phenyl bromide and phenylacetylene. Tetrakis(triphenylphosphano)palladium was used as a catalyst and <i>sec</i>-butylamine as a base. The reaction mechanism was studied in dichloromethane solution. Oxidative addition proceeds through the biligated pathway, and the catalytically active palladium species is Pd(PPh₃)₃. Amines, present in the reaction mixture, can inhibit oxidative addition by coordinating to Pd(PPh₃)₃