Mercury Methylation by Cobalt Corrinoids: Relativistic Effects Dictate the Reaction Mechanism

The methylation of Hg^II(SCH₃)₂ by corrinoid‐based methyl donors proceeds in a concerted manner through a single transition state by transfer of a methyl radical, in contrast to previously proposed reaction mechanisms. This reaction mechanism is a consequence of relativistic effects that lower the energies of the mercury 6p_1/2 and 6p_3/2 orbitals, making them energetically accessible for chemical bonding. In the absence of spin–orbit coupling, the predicted reaction mechanism is qualitatively different. This is the first example of relativity being decisive for the nature of an observed enzymatic reaction mechanism.     

Theoretical Investigation of the OH.‐Initiated Oxidation of Benzaldehyde in the Troposphere

A mechanistic and kinetic study of the OH^.‐initiated oxidation of benzaldehyde is carried out using quantum chemical methods and classical transition state theory. We calculate the rate constant for this reaction within the temperature range of 200–350 K at atmospheric pressure. All possible hydrogen abstraction and OH^. addition channels are considered and branching ratios are obtained. Tunneling corrections are taken into account for abstraction channels, assuming unsymmetrical Eckart barriers. The aldehydic abstraction is by far the most important reaction channel within the entire range of temperatures studied, especially at room temperature and lower—the temperatures relevant to atmospheric chemistry. The relative importance of all the other possible channels increases slightly with temperature. Branching ratios show that addition at the ring and abstraction of an ortho hydrogen contribute about 1 % each at about 300 K, while the branching ratio for the main reaction decreases from 99 % at 200 K to 93 % at 350 K. The results are compared with available experimental measurements.     

DFT Calculations Suggest a New Type of Self‐Protection and Self‐Inhibition Mechanism in the Mammalian Heme Enzyme Myeloperoxidase: Nucleophilic Addition of a Functional Water rather than One‐Electron Reduction

The mammalian heme enzyme myeloperoxidase (MPO) catalyzes the reaction of Cl^? to the antimicrobial‐effective molecule HOCl. During the catalytic cycle, a reactive intermediate “Compound I” (Cpd I) is generated. Cpd I has the ability to destroy the enzyme. Indeed, in the absence of any substrate, Cpd I decays with a half‐life of 100 ms to an intermediate called Compound II (Cpd II), which is typically the one‐electron reduced Cpd I. However, the nature of Cpd II, its spectroscopic properties, and the source of the additional electron are only poorly understood. On the basis of DFT and time‐dependent (TD)‐DFT quantum chemical calculations at the PBE0/6‐31G* level, we propose an extended mechanism involving a new intermediate, which allows MPO to protect itself from self‐oxidation or self‐destruction during the catalytic cycle. Because of its similarity in electronic structure to Cpd II, we named this intermediate Cpd II′. However, the suggested mechanism and our proposed functional structure of Cpd II′ are based on the hypothesis that the heme is reduced by charge separation caused by reaction with a water molecule, and not, as is normally assumed, by the transfer of an electron. In the course of this investigation, we found a second intermediate, the reduced enzyme, towards which the new mechanism is equally transferable. In analogy to Cpd II′, we named it Fe^II′. The proposed new intermediates Cpd II′ and Fe^II′ allow the experimental findings, which have been well documented in the literature for decades but not so far understood, to be explained for the first time. These encompass a) the spontaneous decay of Cpd I, b) the unusual (chlorin‐like) UV/Vis, circular dichroism (CD), and resonance Raman spectra, c) the inability of reduced MPO to bind CO, d) the fact that MPO‐Cpd II reduces SCN^? but not Cl^?, and e) the experimentally observed auto‐oxidation/auto‐reduction features of the enzyme. Our new mechanism is also transferable to cytochromes, and could well be viable for heme enzymes in general.     

Ion‐Pair SN2 Substitution: Activation Strain Analyses of Counter‐Ion and Solvent Effects

The ion‐pair S_N2 reactions of model systems M_nF^n?1+CH₃Cl (M⁺=Li⁺, Na⁺, K⁺, and MgCl⁺; n=0, 1) have been quantum chemically explored by using DFT at the OLYP/6‐31++G(d,p) level. The purpose of this study is threefold: 1) to elucidate how the counterion M⁺ modifies ion‐pair S_N2 reactivity relative to the parent reaction F^?+CH₃Cl; 2) to determine how this influences stereochemical competition between the backside and frontside attacks; and 3) to examine the effect of solvation on these ion‐pair S_N2 pathways. Trends in reactivity are analyzed and explained by using the activation strain model (ASM) of chemical reactivity. The ASM has been extended to treat reactivity in solution. These findings contribute to a more rational design of tailor‐made substitution reactions.     

Competitive Reaction Pathways for the Gas‐Phase Reactivity of [Me2AlNH2]3

Reaction energy profiles for [Me₂AlNH₂]₃ have been computationally explored by using density functional theory. Both intra‐ and intermolecular methane elimination reactions, as well as Al?N bond‐breaking pathways, were considered. The results show that the energy required for Al?N bond breaking in cyclic [Me₂AlNH₂]₃ is of the same order of magnitude as the activation energies for the first (limiting) step of methane elimination (for both mono‐ and bimolecular mechanisms). Thus, dissociative and associative reaction pathways are competitive. Low‐temperature/high‐pressure conditions will favor the bimolecular pathway, whereas at high temperatures, either intramolecular methane elimination or Al?N bond‐breaking dissociative pathways will be operational.     

Mechanistic Insights into the Rhenium‐Catalyzed Alcohol‐To‐Olefin Dehydration Reaction

Rhenium‐based complexes are powerful catalysts for the dehydration of various alcohols to the corresponding olefins. Here, we report on both experimental and theoretical (DFT) studies into the mechanism of the rhenium‐catalyzed dehydration of alcohols to olefins in general, and the methyltrioxorhenium‐catalyzed dehydration of 1‐phenylethanol to styrene in particular. The experimental and theoretical studies are in good agreement, both showing the involvement of several proton transfers, and of a carbenium ion intermediate in the catalytic cycle.     

Insights into the Mechanism of the Reaction between Tetrachloro‐p‐Benzoquinone and Hydrogen Peroxide and their Implications in the Catalytic Role of Water Molecules in Producing the Hydroxyl Radial

Detailed mechanisms for the formation of hydroxyl or alkoxyl radicals in the reactions between tetrachloro‐p‐benzoquinone (TCBQ) and organic hydroperoxides are crucial for better understanding the potential carcinogenicity of polyhalogenated quinones. Herein, the mechanism of the reaction between TCBQ and H₂O₂ has been systematically investigated at the B3LYP/6‐311++G** level of theory in the presence of different numbers of water molecules. We report that the whole reaction can easily take place with the assistance of explicit water molecules. Namely, an initial intermediate is formed first. After that, a nucleophilic attack of H₂O₂ onto TCBQ occurs, which results in the formation of a second intermediate that contains an OOH group. Subsequently, this second intermediate decomposes homolytically through cleavage of the O? O bond to produce a hydroxyl radical. Energy analyses suggest that the nucleophilic attack is the rate‐determining step in the whole reaction. The participation of explicit water molecules promotes the reaction significantly, which can be used to explain the experimental phenomena. In addition, the effects of F, Br, and CH₃ substituents on this reaction have also been studied.     

Multiple Reaction Pathways in Rhodium‐Catalyzed Hydrosilylations of Ketones

A detailed density functional theory (DFT) computational study (using the BP86/SV(P) and B3LYP/TZVP//BP86/SV(P) level of theory) of the rhodium‐catalyzed hydrosilylation of ketones has shown three mechanistic pathways to be viable. They all involve the generation of a cationic complex [L_nRh^I]⁺ stabilized by the coordination of two ketone molecules and the subsequent oxidative addition of the silane, which results in the Rh–silyl intermediates [L_nRh^III(H)SiHMe₂]⁺. However, they differ in the following reaction steps: in two of them, insertion of the ketone into the Rh? Si bond occurs, as previously proposed by Ojima et al., or into the Si? H bond, as proposed by Chan et al. for dihydrosilanes. The latter in particular is characterized by a very high activation barrier associated with the insertion of the ketone into the Si? H bond, thereby making a new, third mechanistic pathway that involves the formation of a silylene intermediate more likely. This “silylene mechanism” was found to have the lowest activation barrier for the rate‐determining step, the migration of a rhodium‐bonded hydride to the ketone that is coordinated to the silylene ligand. This explains the previously reported rate enhancement for R₂SiH₂ compared to R₃SiH as well as the inverse kinetic isotope effect (KIE) observed experimentally for the overall catalytic cycle because deuterium prefers to be located in the stronger bond, that is, C? D versus M? D.     

Synthesis of Cyclooctatetraenes through a Palladium‐Catalyzed Cascade Reaction

Reported is a cascade reaction leading to fully substituted cyclooctatetraenes. This unexpected transformation likely proceeds through a unique 8π electrocyclization reaction of a ene triyne. DFT computations provide the mechanistic basis of this surprizing reaction.     

On the Reaction of Glycerol Dehydratase with But‐3‐ene‐1,2‐diol

Intriguing inactivation : Calculations suggest that the ability of relatively high‐energy radical intermediates to inactivate glycerol dehydratase (GDH) may reflect a general and hitherto unidentified inactivation mechanism in the reaction of coenzyme B₁₂‐dependent enzymes and 3‐unsaturated 1,2‐diols (see scheme; AdoCbl: adenosylcobalamin or coenzyme B₁₂).

     

Enantioselective Arylation of N‐Tosylimines by Phenylboronic Acid Catalysed by a Rhodium/Diene Complex: Reaction Mechanism from Density Functional Theory

A DFT study of the reaction mechanism of the rhodium‐catalysed enantioselective arylation of (E)‐N‐propylidene‐4‐methyl‐benzenesulfonamide by phenylboronic acid [Lin et al J. Am. Chem. Soc.­ 2011 , 133, 12394] is reported. The catalyst ([{Rh(OH)(diene)}₂]) includes a chiral diene ligand and the reaction is conducted in 1,4‐dioxane in the presence of drying agents (4 Å molecular sieves). Because phenylboronic acid is in equilibrium with phenylboroxin and water under the reaction conditions, three catalytic cycles are proposed that differ in the way the transmetallation and the release of the product are brought about, depending on the availability of phenylboronic acid, water and boroxin in the reaction medium. Based on computations, a new mechanism for the title reaction is proposed, in which phenylboronic acid plays the double role of “aryl source” and proton donor. This path does not require the presence of adventitious water molecules, in keeping with a reaction conducted in a dry medium. Comparisons with the generally accepted mechanism for arylation of enones proposed by Hayashi and co‐workers (J. Am. Chem. Soc.­ 2002 , 124, 5052) show that the latter mechanism is less favourable and is not expected to operate in the case of the N‐tosylimine substrate considered herein. Finally, the possibility that phenylboroxin is the aryl source has also been investigated, but is not found to be competitive.     

The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase

Atomic‐level portrait : The mechanism of the reaction catalyzed by the puzzling enzyme farnesyltransferase is elucidated by using computational methods, allowing the obtainment of the first real detailed atomistic quantum‐chemical transition‐state structure (see figure) for the reaction catalyzed by this enzyme. The results obtained provide an atomic‐level framework for the design of more potent and specific inhibitors for this important enzyme.

     

Triesterase and Promiscuous Diesterase Activities of a Di‐CoII‐Containing Organophosphate Degrading Enzyme Reaction Mechanisms

The reaction mechanism for the hydrolysis of trimethyl phosphate and of the obtained phosphodiester by the di‐Co^II derivative of organophosphate degrading enzyme from Agrobacterium radiobacter P230(OpdA), have been investigated at density functional level of theory in the framework of the cluster model approach. Both mechanisms proceed by a multistep sequence and each catalytic cycle begins with the nucleophilic attack by a metal‐bound hydroxide on the phosphorus atom of the substrate, leading to the cleavage of the phosphate‐ester bond. Four exchange‐correlation functionals were used to derive the potential energy profiles in protein environments. Although the enzyme is confirmed to work better as triesterase, as revealed by the barrier heights in the rate‐limiting steps of the catalytic processes, its promiscuous ability to hydrolyze also the product of the reaction has been confirmed. The important role played by water molecules and some residues in the outer coordination sphere has been elucidated, while the binuclear Co^II center accomplishes both structural and catalytic functions. To correctly describe the electronic configuration of the d shell of the metal ions, high‐ and low‐spin arrangement jointly with the occurrence of antiferromagnetic coupling, have been herein considered.     

Mechanism of the Asymmetric Autocatalytic Soai Reaction Studied by Density Functional Theory

The mechanism of the Soai reaction has been thoroughly investigated at the M05‐2X/6‐31G(d) level of theory, by considering ten energetically distinct paths. The study indicates the fully enantioselective catalytic cycle of the homochiral dimers to be the dominant mechanism. Two other catalytic cycles are shown to both be important for correct understanding of the Soai reaction. These are the catalytic cycle of the heterochiral dimer and the non‐enantioselective catalytic cycle of the homochiral dimers. The former has been proved to be not really competitive with the principal cycle, as required for the Soai reaction to manifest chiral amplification, whereas the latter, which is only slightly competitive with the principal one, nicely explains the experimental enantioselectivity observed in the reaction of 2‐methylpyrimidine‐5‐carbaldehyde. The study has also evidenced the inadequacy of the B3LYP functional for mechanistic investigations of the Soai reaction.     

Theoretical Study of the Cycloaddition Reaction of a Tungsten‐Containing Carbonyl Ylide

The [3+2] cycloaddition reaction of a tungsten‐containing carbonyl ylide with methyl vinyl ether and the insertion reactions of the nonstabilized carbene complex intermediates produced have been investigated through the use of B3LYP density functional theory. The [3+2] cycloaddition reaction of the tungsten‐containing carbonyl ylide has been proven to proceed concertedly, reversibly, and with high endo selectivity. The intermolecular Si? H insertion reactions of the carbene complex intermediates have been proven to be favored over the intramolecular C? H insertion, in good agreement with experimental results. Moreover, the kinetic endo/exo ratio of the [3+2] cycloaddition reaction has been shown to determine the endo/exo selectivity of the Si? H insertion products. In addition, secondary orbital interactions involving the benzene ring and the carbonyl ligand on the metal center have turned out to strongly influence the high endo selectivity of the [3+2] cycloaddition reaction with methyl vinyl ether.