DFT studies of the degradation mechanism of methyl mercury activated by a sulfur-rich ligand

Light-Triggered Metal Coordination Dynamics in Photoswitchable Dithienylethene-Ferrocene System

The C₂-symmetric photochromic molecule 3, containing dithienylethene (DTE) and ferrocene units connected by an alkyne bridge, represents a unique probe where a metal (Hg²⁺) binds with the central DTE moiety. Both photoisomerized states of 3 (open, 3o; closed, 3c) are found to interact with Hg²⁺ ion by the S atoms of the DTE core; however, the binding constants (from a UV-vis study) and DFT calculations suggest that the open isomer (3o) binds with the metal ion more strongly than that of the closed isomer (3c). Notably, the course of metal binding does not perturb the inherent photoisomerization properties of the DTE core and the photoswitchability persists even in the metal-coordinated form of 3, however, with a comparatively slower rate. The quantum yields for photocyclization (Φ_o→c) and photocycloreversion (Φ_c→o) in the free form are 0.56 and 0.007, respectively, whereas the photocyclization quantum yield in the Hg²⁺ complexed species is 0.068, 8.2 times lower than the photocyclization quantum yield (Φ_o→c) of free 3o. Thus, the rate of photoisomerization can be modulated by a suitable metal coordination to the DTE core. The dynamics of photoswitchability in the metal-coordinated form of DTE has been explored by experimental means (UV-vis and electrochemical studies) as well as quantum chemical calculations.

Hg-C bond protonolysis by a functional model of bacterial enzyme organomercurial lyase MerB

Herein, we report a novel synthetic compound 1, having a highly nucleophilic selenolate (Se^-) moiety and a thiol (-SH) functional group, which showed efficient Hg-C bond protonolysis of various R-Hg-X molecules including neurotoxic methylmercury and thimerosal, via direct -SH proton transfer to the highly activated C-atom of a departed R group with low activation energy barrier at room temperature (21 °C), in the absence of any external proton source and, thus, acts as a functional model of MerB.

Mechanistic pathways of mercury removal from the organomercurial lyase active site

Bacterial populations present in Hg-rich environments have evolved biological mechanisms to detoxify methylmercury and other organometallic mercury compounds. The most common resistance mechanism relies on the H⁺-assisted cleavage of the Hg–C bond of methylmercury by the organomercurial lyase MerB. Although the initial reaction steps which lead to the loss of methane from methylmercury have already been studied experimentally and computationally, the reaction steps leading to the removal of Hg²⁺ from MerB and regeneration of the active site for a new round of catalysis have not yet been elucidated. In this paper, we have studied the final steps of the reaction catalyzed by MerB through quantum chemical computations at the combined MP2/CBS//B3PW91/6-31G(d) level of theory. While conceptually simple, these reaction steps occur in a complex potential energy surface where several distinct pathways are accessible and may operate concurrently. The only pathway which clearly emerges as forbidden in our analysis is the one arising from the sequential addition of two thiolates to the metal atom, due to the accumulation of negative charges in the active site. The addition of two thiols, in contrast, leads to two feasible mechanistic possibilities. The most straightforward pathway proceeds through proton transfer from the attacking thiol to Cys159 , leading to its removal from the mercury coordination sphere, followed by a slower attack of a second thiol, which removes Cys96. The other pathway involves Asp99 in an accessory role similar to the one observed earlier for the initial stages of the reaction and affords a lower activation enthalpy, around 14 kcal mol⁻¹, determined solely by the cysteine removal step rather than by the thiol ligation step. Addition of one thiolate to the intermediates arising from either thiol attack occurs without a barrier and produces an intermediate bound to one active site cysteine and from which Hg(SCH₃)₂ may be removed only after protonation by solvent-provided H₃O⁺. Thiolate addition to the active site (prior to any attack by thiols) leads to pathways where the removal of the first cysteine becomes the rate-determining step, irrespective of whether Cys159 or Cys96 leaves first. Comparisons with the recently computed mechanism of the related enzyme MerA further underline the important role of Asp99 in the energetics of the MerB reaction. Kinetic simulation of the mechanism derived from our computations strongly suggests that in vivo the thiolate-only pathway is operative, and the Asp-assisted pathway (as well as the conversion of intermediates of the thiolate pathway into intermediates of the Cys-assisted pathway) is prevented by steric factors absent from our model and related to the precise geometry of the organomercurial binding-pocket.

Complexation of some alkali and alkaline earth metal cations by macrocyclic compounds containing four pyridine subunits – a DFT study

Tetradentate pyridine-based macrocyclic compounds offer useful ligands capable of efficient and selective complexation of M = Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺and Ca²⁺.

Theoretical study on the chemical mechanism of enoyl-CoA hydratase and the form of inhibitor binding

Enoyl-CoA hydratase (ECH) catalyzes the second step in the vital β-oxidation pathway of fatty acid metabolism. This enzyme catalyzes the syn-addition of a water molecule across the double bond of 4-(N,N-dimethylamino) cinnamoyl-CoA (DAC-CoA). In this work, the reaction mechanisms of ECH were investigated using the density functional theory (DFT) methods. The different protonation states in which the important residues Glu164 and Glu144 are either neutral or ionized were considered. Four models of the active site were designed based on the X-ray crystal structure of the enzyme. The calculations gave strong support to the proposed mechanism and confirmed that both Glu164 and Glu144 are in a deprotonated state in the reaction mechanism of ECH. In addition, we constructed a model of the active site with the inhibitor acetoacetyl-CoA based on the crystal structure. Caomparison of the calculated energy barriers showed that binding of the keto-enol form of the inhibitor is more reasonable than that of the di-keto form in the inhibition process. Moreover, acetoacetyl-CoA was found to exhibit a keto-enol tautomerism when it acts as an inhibitor in the reaction. The present theoretical results indicated that both residues Glu164 and Glu144 are unprotonated in ECH with the substrate bound, while only Glu164 is unprotonated when the inhibitor binds ECH.