Theoretical study of a derivative of chlorophosphine with aliphatic and aromatic Grignard reagents: SN2@P or the novel SN2@Cl followed by SN2@C?

The proposed SN2 reactions of a hindered organophosphorus reactant with aliphatic and aromatic nucleophiles [Ye et al., Org. Lett., 2017, 19, 5384-5387] were studied theoretically in order to explain the observed stereochemistry of the products. Our computations (using B3LYP as the functional) indicate that the reaction with the aliphatic nucleophile occurs through a backside SN2@P pathway while the reaction with the aromatic nucleophile proceeds through a novel SN2@Cl mechanism, followed by a frontside SN2@C mechanism.

Theoretical study of the interactions between peptide tyrosine tyrosine [PYY (1-36)], a newly identified modulator in type 2 diabetes pathophysiology, with receptors NPY1R and NPY4R.

PURPOSE: Diabetes mellitus is a common condition in the clinically obese. Bariatric surgery is one of the ways to put type 2 diabetes in remission. Recent findings propose the appetite-regulator peptide tyrosine tyrosine (PYY) as a therapeutic option for patients with type 2 diabetes. This novel gut hormone restores impaired insulin and glucagon secretion in pancreatic islets and is implicated in type 2 diabetes reversal after bariatric surgery. The current study elucidates the interactions between PYY and the NPY1R and NPY4R receptors using computational methods. METHODS: Protein structure prediction, molecular docking simulation, and molecular dynamics (MD) simulation were performed to elucidate the interactions of PYY with NPY1R and NPY4R. RESULTS: The predicted binding models of PYY-NPY receptors are in agreement with those described in the literature, although different interaction partners are presented for the C-terminal tail of PYY. Non-polar interactions are predicted to drive the formation of the protein complex. The calculated binding energies show that PYY has higher affinity for NPY4R (ΔGGBSA = -65.08 and ΔGPBSA = -87.62 kcal/mol) than for NPY1R (ΔGGBSA = -23.11 and ΔGPBSA = -50.56 kcal/mol). CONCLUSIONS: Based on the constructed models, the binding conformations obtained from docking and MD simulation for both the PYY-NPY1R and PYY-NPY4R complexes provide a detailed map of possible interactions. The calculated binding energies show a higher affinity of PYY for NPY4R. These findings may help to understand the mechanisms behind the improvement of diabetes following bariatric surgery.

Activation Strain Analyses of Counterion and Solvent Effects on the Ion-Pair SN 2 Reaction of NH 2 - and CH3 Cl.

We have computationally studied the bimolecular nucleophilic substitution (SN 2) reactions of Mn NH2 (n-1) + CH3 Cl (M+ = Li+ , Na+ , K+ , and MgCl+ ; n = 0, 1) in the gas phase and in tetrahydrofuran solution at OLYP/6-31++G(d,p) using polarizable continuum model implicit solvation. We wish to explore and understand the effect of the metal counterion M+ and of solvation on the reaction profile and the stereochemical preference, that is, backside (SN 2-b) versus frontside attack (SN 2-f). The results were compared to the corresponding ion-pair SN 2 reactions involving F- and OH- nucleophiles. Our analyses with an extended activation strain model of chemical reactivity uncover and explain various trends in SN 2 reactivity along the nucleophiles F- , OH- , and NH 2 - , including solvent and counterion effects. © 2019 Wiley Periodicals, Inc.

A theoretical study of the hydrolysis mechanism of A-234; the suspected novichok agent in the Skripal attack.

A-234, [EtO-P([double bond, length as m-dash]O)(F)-N[double bond, length as m-dash]C(Me)-N(Et)2], is the suspected A-type nerve agent used in the Skripal attack on the 4th of March 2018. Studies related to the structure and reactivity of this compound are limited. We, therefore, aimed at understanding the underlying hydrolysis mechanism of A-234 within the DFT framework. The attack of the water molecule can occur at the phosphinate and acetoamidine reactive centres. Our theoretical findings indicate that the hydrolysis at the acetoamidine centre is thermodynamically favoured compared to the hydrolysis at the phosphinate centre. The hydrolysis at the acetoamidine moiety may proceed via two pathways, depending on the nitrogen atom participating in the hydrolysis. The main pathway consists of four distinct channels to reach the final product, with the concerted 1,3-proton shift favoured kinetically and thermodynamically in the gas phase and water as solvent. The results are in good agreement with the literature, although some differences in the reaction mechanism were observed.

ExcelAutomat 1.3: Fragment analysis based on the distortion/interaction-activation strain model.

The distortion/interaction-activation strain model (D/I-ASM), a fragment analysis method, is applied to study the structure-reactivity relationship in reactions. The application of D/I-ASM involves the generation of input files for points along a reaction profile, submission of input files to a quantum software package, processing of parameters from the resulting output files and generation of graphical plots. The ExcelAutomat tool (Laloo et al., J. Comput. Aided Mol. Des. 2017, 31, 667) provides a framework and library in Visual Basic for Application programming language to process such files. New routines were written in ExcelAutomat 1.3 to facilitate processing of files for D/I-ASM. The worksheet "ASM" was included where initial parameters needed can be defined. The routines for D/I-ASM were tested successfully on bimolecular nucleophilic substitution, cycloaddition, and barrierless reactions. The automation of fragment analysis by ExcelAutomat 1.3 is compatible with Microsoft Excel and LibreOffice Calc. The extensible tool processes files from Gaussian and GAMESS-US packages. © 2018 Wiley Periodicals, Inc.