Nucleophilic Neutralization of Organophosphates: Lack of Selectivity or Plenty of Versatility?

Neutralization of organophosphates is an issue of public health and safety, involving agrochemicals and chemical warfare. A promising approach is the nucleophilic neutralization, scope of this review, which focuses on the molecular nucleophiles: hydroxide, imidazole derivatives, alpha nucleophiles, amines and other nucleophiles. A reactivity mapping is given correlating the pathways and reaction efficiency with structural dependence of the nucleophile (basicity) and the organophosphate (electrophilic centers, P=O/P=S shift, leaving and non-leaving group). Reactions extremely unfavorable (>20 years) can be reduced to seconds with various nucleophiles, some which are catalytic. Although there is no universal nucleophile, a lack of selectivity in some cases accounts for plenty of versatility in other reactions. The ideal neutralization requires a solid mechanistic understanding, together with balancing factors such as milder conditions, fast process, selectivity and less toxic products.

A computational study of the reaction mechanism involved in the fast cleavage of an unconstrained amide bond assisted by an amine intramolecular nucleophilic attack

In the present work, the fast amide bond cleavage of [3-((1R,5S,7s)-3-azabicyclo[3.3.1]nonane-7-carbonyl)-3-azabicyclo[3.3.1]nonane-7-carboxylic acid (bi-ATDO)], through an intramolecular nucleophilic attack of an amine group is evaluated. First, six possible peptide bond cleavage mechanisms, two of them including a water molecule, are described at the ωB97XD/6-311 + G(d,p)//MP2/6-311 + G(d,p) level of theory. The reaction consisting of an intramolecular nitrogen nucleophilic attack followed by a proton transfer and the amide bond cleavage is determined as the most favorable mechanism. The activation free energy computed for the latter is 20.5 kcal mol^-1 , which agrees with the reported experimental result of 24.8 kcal mol^-1 . Inclusion of a water molecule to assist the first step of the reaction results in an activation free energy increase of about 17 kcal mol^-1 . All the steps in the most favorable mechanism are studied more in detail employing intrinsic reaction coordinate as well as the reaction force and reaction electronic flux analysis.

Electrophilic activation of aminocarboxylic acid by phosphate ester promotes Friedel-Crafts acylation by overcoming charge-charge repulsion

Friedel-Crafts acylation of aromatic compounds with aminocarboxylic acids proceeds efficiently in the presence of a tailored phosphate ester and a strong Brønsted acid, despite the strong charge-charge repulsion associated with acylium ion formation. Here, we investigate the mechanism of this electrophilic aromatic acylation reaction, focusing on how the aminocarboxylic acid is activated by the phosphate ester and how the charge-charge repulsion is overcome. In the first step of the reaction, an acyl phosphate is generated from the aminocarboxylic acid through the intervention of the phosphate ester, which possesses three methyl salicylate ester linkages. The o-methyl salicylates enhance the reactivity of the phosphate ester via a protonation-induced conformational change, thereby overwhelming the charge-charge repulsion associated with the acylium ion formation. Weakening of the resonance interaction in the C(O)-O(P) bond by the lone-pair electrons of the ether oxygen atom of the carboxylic acid functionality contributes to the rapid formation of the acylium ion. Thus, our results show that the formation of aromatic ketones from various carboxylic acids proceeds because the strong leaving ability of the acyl phosphate overwhelms the charge-charge repulsion associated with the formation of the acylium ion. This information will be helpful to improve the design of tailored phosphate reagents.

Reactivity and selectivity of the reaction of O,O-diethyl 2,4-dinitrophenyl phosphate and thionophosphate with thiols of low molecular weight

A kinetics control product by sulfhydryl attack of thiols was observed in the reactions of both triesters with Cys and Hcys, followed by an intramolecular amine attack leading to a thermodynamic control product.

A Theoretical Study of Phosphoryl Transfers of Tyrosyl-DNA Phosphodiesterase I (Tdp1) and the Possibility of a "Dead-End" Phosphohistidine Intermediate

Tyrosyl-DNA phosphodiesterase I (Tdp1) is a DNA repair enzyme conserved across eukaryotes that catalyzes the hydrolysis of the phosphodiester bond between the tyrosine residue of topoisomerase I and the 3'-phosphate of DNA. Atomic level details of the mechanism of Tdp1 are proposed and analyzed using a fully quantum mechanical, geometrically constrained model. The structural basis for the computational model is the vanadate-inhibited crystal structure of human Tdp1 (hTdp1, Protein Data Bank entry 1RFF ). Density functional theory computations are used to acquire thermodynamic and kinetic data along the catalytic pathway, including the phosphoryl transfer and subsequent hydrolysis. Located transition states and intermediates along the reaction coordinate suggest an associative phosphoryl transfer mechanism with five-coordinate phosphorane intermediates. Similar to both theoretical and experimental results for phospholipase D, the proposed mechanism for hTdp1 also includes the thermodynamically favorable possibility of a four-coordinate phosphohistidine "dead-end" product.

The role of ammonia oxide in the reaction of hydroxylamine with carboxylic esters

Hydroxylamine can form a stable zwitterionic isomer that is a key for its high reactivity.

In silico study on the mechanism of formation of hydrazine and nitrogen in the reactions of excess hydroxylamine with 2,4-dinitrophenyl diethyl phosphate

Decomposition study of 2,4-dinitrophenyl diethyl phosphate to hydrazine and nitrogen gas with excess of hydroxylamine using quantum chemical calculations.