Reaction mechanism of apocarotenoid oxygenase (ACO): a DFT study

The mechanism of the oxidative cleavage catalyzed by apocarotenoid oxygenase (ACO) was studied by using a quantum chemical (DFT: B3 LYP) method. Based on the available crystal structure, relatively large models of the unusual active-site region, in which a ferrous ion is coordinated by four histidines and no negatively charged ligand, were selected and used in the computational investigation of the reaction mechanism. The results suggest that binding of dioxygen to the ferrous ion in the active site promotes one-electron oxidation of carotenoid leading to a substrate radical cation and a Fe-bound superoxide radical. Recombination of the two radicals, which can be realized in at least two different ways, yields a reactive peroxo species that subsequently evolves into either a dioxetane or an epoxide intermediate. The former easily decays into the final aldehyde products, whereas the oxidation of the epoxide to the proper products of the reaction requires involvement of a water molecule. The calculated activation barriers favor the dioxetane mechanism, yet the mechanism involving the epoxide intermediate cannot be ruled out.     

Regioselectivity in the Intramolecular Heck Reaction of a Series of Cyclic Sulfonamides: An Experimental and Computational Study

Regioselectivity in the intramolecular Heck reaction of a series of N‐sulfonyl‐2,5‐dihydro‐3‐substituted pyrroles was studied. These substrates are unbiased in terms of the formed ring size of the new heterocycle. Results indicate that high levels of regioselectivity are observed under a range of conditions, and that there is an underlying propensity for carbon–carbon bond formation at the most hindered end of the alkene. For two examples (3‐Me and 3‐tBu), DFT calculations were performed and indicate that in both cases, the modelled transition state for carbopalladation is energetically lower for the experimentally preferred isomer.     

Transmetalation reactions from Fischer carbene complexes to late transition metals: a DFT study

Transmetalation reactions from chromium(0) Fischer carbene complexes to late-transition-metal complexes (palladium(0), copper(I), and rhodium(I)) have been studied computationally by density functional theory. The computational data were compared with the available experimental data. In this study, the different reaction pathways involving the different metal atoms have been compared with each other in terms of their activation barriers and reaction energies. Although the reaction profiles for the transmetalation reactions to palladium and copper are quite similar, the computed energy values indicate that the process involving palladium as catalyst is more favorable than that involving copper. In contrast to these transformations, which occur via triangular heterobimetallic species, the transmetalation reaction to rhodium leads to a new heterobimetallic species in which a carbonyl ligand is also transferred from the Fischer carbene to the rhodium catalyst. Moreover, the structure and bonding situation of the so far elusive heterobimetallic complexes are briefly discussed.     

The Computational Road to Better Catalysts

Computational studies, especially those that use density functional theory (DFT), have become pervasive in the characterization, mechanistic study, and optimization of homogeneous organometallic catalysts, and the “rational” design of such catalysts seems within reach once more. But how advanced, user‐friendly, and reliable are the computational tools that are currently available? Here we summarize the current state of the art for predictive computational organometallic chemistry in reference to the different stages of catalyst development by considering characterization, mechanistic studies, fine‐tuning/optimization, and evaluation of novel designs. We also assess critically where the strengths and weaknesses of computational studies lie and hence map out the road ahead for the design and discovery of novel catalysts in silico and in combination with targeted experimental studies.     

Phosphate Monoester Hydrolysis by Trinuclear Alkaline Phosphatase; DFT Study of Transition States and Reaction Mechanism

Alkaline phosphatase (AP) is a trinuclear metalloenzyme that catalyzes the hydrolysis of a broad range of phosphate monoesters to form inorganic phosphate and alcohol (or phenol). In this paper, by using density functional theory with a model based on a crystal structure, the AP‐catalyzed hydrolysis of phosphate monoesters is investigated by calculating two substrates, that is, methyl and p‐nitrophenyl phosphates, which represent alkyl and aryl phosphates, respectively. The calculations confirm that the AP reaction employs a “ping‐pong” mechanism involving two chemical displacement steps, that is, the displacement of the substrate leaving group by a Ser102 alkoxide and the hydrolysis of the phosphoseryl intermediate by a Zn2‐bound hydroxide. Both displacement steps proceed via a concerted associative pathway no matter which substrate is used. Other mechanistic aspects are also studied. Comparison of our calculations with linear free energy relationships experiments shows good agreement.     

The Roles of Counterion and Water in a Stereoselective Cysteine‐Catalyzed Rauhut–Currier Reaction: A Challenge for Computational Chemistry

The stereoselective Rauhut–Currier (RC) reaction catalyzed by a cysteine derivative has been explored computationally with density functional theory (M06‐2X). Both methanethiol and a chiral cysteine derivative were studied as nucleophiles. The complete reaction pathway involves rate‐determining elimination of the thiol catalyst from the Michael addition product. The stereoselective Rauhut–Currier reaction, catalyzed by a cysteine derivative as a nucleophile, has also been studied in detail. This reaction was experimentally found to be extremely sensitive to the reaction conditions, such as the number of water equivalents and the effect of potassium counterion. The E1cB process for catalyst elimination has been explored computationally for the eight possible stereoisomers. The effect of explicit water solvation and the presence of counterion (either K⁺ or Na⁺) has been studied for the lowest energy enantiomer pair (1S, 2R, 3S)/(1R, 2S, 3R).     

Computational Investigation of the Effect of pH on the Color of Firefly Bioluminescence by DFT

In spite of recent advances towards understanding the mechanism of firefly bioluminescence, there is no consensus about which oxyluciferin (OxyLH₂) species are the red and yellow‐green emitters. The crystal structure of Luciola cruciata luciferase (LcLuc) revealed different conformations for the various steps of the bioluminescence reaction, with different degrees of polarity and rigidity of the active‐site microenvironment. In this study, these different conformations of luciferase (Luc) are simulated and their effects on the different chemical equilibria of OxyLH₂ are investigated as a function of pH by means of density functional theory with the PBE0 functional. In particular, the thermodynamic properties and the absorption spectra of each species, as well as their relative stabilities in the ground and excited states, were computed in the different conformations of Luc. From the calculations it is possible to derive the acid dissociation and tautomeric constants, and the corresponding distribution diagrams. It is observed that the anionic keto form of OxyLH₂ is both the red and the yellow‐green emitter. Consequently, the effect of Luc conformations on the structural and electronic properties of the Keto‐(?1) form are studied. Finally, insights into the Luc‐catalyzed light‐emitting reaction are derived from the calculations. The multicolor bioluminescence can be explained by interactions of the emitter with active‐site molecules, the effects of which on light emission are modulated by the internal dielectric constant of the different conformations. These interactions can suffer also from rearrangement due to entry of external solvent and changes in the protonation state of some amino acid residues and adenosine monophosphate (AMP).     

Comparison of Cu‐ZSM‐5 Zeolites and Cu‐MOF‐505 Metal‐Organic Frameworks as Heterogeneous Catalysts for the Mukaiyama Aldol Reaction: A DFT Mechanistic Study

The density functional theory (DFT) model ONIOM(M06L/6‐311++G(2df,2p):UFF was employed to reveal the catalytic activity of Cu^II in the paddle‐wheel unit of the metal‐organic framework (MOF)‐505 material in the Mukaiyama aldol reaction compared with the activity of Cu‐ZSM‐5 zeolites. The aldol reaction between a silyl enol ether and formaldehyde catalyzed by the Lewis acidic site of both materials takes place through a concerted pathway, in which the formation of the C? C bond and the transfer of the silyl group occurs in a single step. MOF‐505 and Cu‐ZSM‐5 are predicted to be efficient catalysts for this reaction as they strongly activate the formaldehyde carbonyl carbon electrophile, which leads to a considerably lower reaction barrier compared with the gas‐phase system. Both MOF‐505 and Cu‐ZSM‐5 catalysts stabilize the reacting species along the reaction coordinate, thereby lowering the activation energy, compared to the gas‐phase system. The activation barriers for the MOF‐505, Cu‐ZSM‐5, and gas‐phase system are 48, 21, and 61 kJ mol^?1, respectively. Our results show the importance of the enveloping framework by stabilizing the reacting species and promoting the reaction.     

Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase

A cyclin-dependent kinase, Cdk2, catalyzes the transfer of the gamma-phosphate from ATP to a threonine or serine residue of its polypeptide substrates. Here, we investigate aspects of the reaction mechanism of Cdk2 by gas-phase density functional calculations, classical molecular dynamics, and Car-Parrinello QM/MM simulations. We focus on the role of the conserved Asp127 and on the nature of the phosphoryl transfer reaction mechanism catalyzed by Cdk2. Our findings suggest that Asp127 is active in its deprotonated form by assisting the formation of the near-attack orientation of the substrate serine or threonine. Therefore, the residue does not act as a general base during the catalysis. The mechanism for the phosphoryl transfer is a single SN2-like concerted step, which shows a phosphorane-like transition state geometry. Although the resulting reaction mechanism is in agreement with a previous density functional study of the same catalytic reaction mechanism (Cavalli et al., Chem. Comm. 2003, 1308-1309), the reaction barrier is considerably lower when QM/MM calculations are performed, as in this study ( approximately 42 kcal mol(-1) QM vs. approximately 24 kcal mol(-1) QM/MM); this indicates that important roles for the catalysis are played by the protein environment and solvent waters. Because of the high amino acid sequence conservation among the whole family of cyclin-dependent kinases (CDKs), these results could be general for the CDK family.     

Computational Study of Benzosultam Formation through Gold(I)-Catalyzed Ammoniumation/Nucleophilic Substitution Reaction

The Au(I)-catalyzed reactions of (2-alkynyl)phenylsulfonyl azetidines bearing terminal and non-terminal alkynes in the presence of methanol as protic nucleophile to form benzosultams derivatives were studied by density functional theory (DFT) calculations. Our study highlights that gold(I) catalyzed nucleophilic addition of the nitrogen on the alkyne is favored over the direct ring opening of the azetidine by methanol, confirming the ammonium-based mechanism. In addition, the reverse regioselectivity observed experimentally where non-terminal alkynes favors the formation of 6-endo-dig-benzosultams while terminal alkynes favor 5-exo-dig products is also explored through two different scenarios. The first one embraces the classical activation of the alkyne by a single Au(I) species while the second one tackles the formation of a σ,π-digold acetylide complex. Calculations identify both pathways as competitive although only mono Au(I) complexes can lead to final products, in good agreement with experimental observation. Further details on the importance of the presence of an excess of the protic nucleophile on the protodemetallation step and the final aminal formation is also discussed.     

Ketene as a Reaction Intermediate in the Carbonylation of Dimethyl Ether to Methyl Acetate over Mordenite

Unprecedented insight into the carbonylation of dimethyl ether over Mordenite is provided through the identification of ketene (CH₂CO) as a reaction intermediate. The formation of ketene is predicted by detailed DFT calculations and verified experimentally by the observation of doubly deuterated acetic acid (CH₂DCOOD), when D₂O is introduced in the feed during the carbonylation reaction.     

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.     

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.     

Hydrogen Release from Dialkylamine–Boranes Promoted by Mg and Ca Complexes: A DFT Analysis of the Reaction Mechanism

Mg and Ca β‐diketiminato silylamides [HC{(Me)CN(2,6‐iPr₂C₆H₃)}₂M(THF)_n{N(SiMe₃)₂}] (M=Mg, n=0; M=Ca, n=1) were studied as precatalysts for the dehydrogenation/dehydrocoupling of secondary amine–boranes R₂HNBH₃. By reaction with equimolar quantities of amine–boranes, the corresponding amidoborane derivatives are formed, which further react to yield dehydrogenation products such as the cyclic dimer [BH₂?NMe₂]₂. DFT was used here to explore the mechanistic alternatives proposed on the basis of the experimental findings for both Mg and Ca amidoboranes. The influence of the steric demand of amine–boranes on the course of the reaction was examined by performing calculations on the dehydrogenation of dimethylamine–borane (DMAB), pyrrolidine–borane (PB), and diisopropylamine–borane. In spite of the analogies in the catalytic activity of Mg‐ and Ca‐based complexes in the dehydrocoupling of amine–boranes, our theoretical analysis confirmed the experimentally observed lower reactivity of Ca complexes. Differences in catalytic activity of Mg‐ and Ca‐based complexes were examined and rationalized. As a consequence of the increase in ionic radius on going from Mg²⁺ to Ca²⁺, the dehydrogenation mechanism changes and formation of a key metal hydride intermediate becomes inaccessible. Dimerization is likely to occur off‐metal in solution for DMAB and PB, whereas steric hindrance of iPr₂NHBH₃ hampers formation of the cyclic dimer. The reported results are of particular interest because, although amine–borane dehydrogenation is now well established, mechanistic insight is still lacking for many systems.     

Multiple Reaction Pathways Operating in the Mechanism of Vinylogous Mannich‐Type Reaction Activated by a Water Molecule

A systematic search for reaction pathways for the vinylogous Mannich‐type reaction was performed by the artificial force induced reaction method. This reaction affords δ‐amino‐γ‐butenolide in one pot by mixing 2‐trimethylsiloxyfuran, imine, and water under solvent‐free conditions. Surprisingly, the search identified as many as five working pathways. Among them, two concertedly produce anti and syn isomers of the product. Another two give an intermediate, which is a regioisomer of the main product. This intermediate can undergo a retro‐Mannich reaction to give a pair of intermediates: an imine and 2‐furanol. The remaining pathway directly generates this intermediate pair. The imine and 2‐furanol easily react with each other to afford the product. Thus, all of these stepwise pathways finally converge to give the main product. The rate‐determining step of all five (two concerted and three stepwise) pathways have a common mechanism: concerted Si? O bond formation through the nucleophilic attack of a water molecule on the silicon atom followed by proton transfer from the water molecule to the imine. Therefore, these five pathways have comparable barriers and compete with each other.     

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.     

Mechanistic Insights into Palladium‐Catalyzed Silylation of Aryl Iodides with Hydrosilanes through a DFT Study

The catalytic cycles of palladium‐catalyzed silylation of aryl iodides, which are initiated by oxidative addition of hydrosilane or aryl iodide through three different mechanisms characterized by intermediates R₃Si−Pd^II−H (Cycle A), Ar−Pd^II−I (Cycle B), and Pd^IV (Cycle C), have been explored in detail by hybrid DFT. Calculations suggest that the chemical selectivity and reactivity of the reaction depend on the ligation state of the catalyst and specific reaction conditions, including feeding order of substrates and the presence of base. For less bulky biligated catalyst, Cycle C is energetically favored over Cycle A, through which the silylation process is slightly favored over the reduction process. Interestingly, for bulky monoligated catalyst, Cycle B is energetically more favored over generally accepted Cycle A, in which the silylation channel is slightly disfavored in comparison to that of the reduction channel. Moreover, the inclusion of base in this channel allows the silylated product become dominant. These findings offer a good explanation for the complex experimental observations. Designing a reaction process that allows the oxidative addition of palladium(0) complex to aryl iodide to occur prior to that with hydrosilane is thus suggested to improve the reactivity and chemoselectivity for the silylated product by encouraging the catalytic cycle to proceed through Cycles B (monoligated Pd⁰ catalyst) or C (biligated Pd⁰ catalyst), instead of Cycle A.     

Mechanistic Investigation of Chiral Phosphoric Acid Catalyzed Asymmetric Baeyer–Villiger Reaction of 3‐Substituted Cyclobutanones with H2O2 as the Oxidant

The mechanism of the chiral phosphoric acid catalyzed Baeyer–Villiger (B–V) reaction of cyclobutanones with hydrogen peroxide was investigated by using a combination of experimental and theoretical methods. Of the two pathways that have been proposed for the present reaction, the pathway involving a peroxyphosphate intermediate is not viable. The reaction progress kinetic analysis indicates that the reaction is partially inhibited by the γ‐lactone product. Initial rate measurements suggest that the reaction follows Michaelis–Menten‐type kinetics consistent with a bifunctional mechanism in which the catalyst is actively involved in both carbonyl addition and the subsequent rearrangement steps through hydrogen‐bonding interactions with the reactants or the intermediate. High‐level quantum chemical calculations strongly support a two‐step concerted mechanism in which the phosphoric acid activates the reactants or the intermediate in a synergistic manner through partial proton transfer. The catalyst simultaneously acts as a general acid, by increasing the electrophilicity of the carbonyl carbon, increases the nucleophilicity of hydrogen peroxide as a Lewis base in the addition step, and facilitates the dissociation of the OH group from the Criegee intermediate in the rearrangement step. The overall reaction is highly exothermic, and the rearrangement of the Criegee intermediate is the rate‐determining step. The observed reactivity of this catalytic B–V reaction also results, in part, from the ring strain in cyclobutanones. The sense of chiral induction is rationalized by the analysis of the relative energies of the competing diastereomeric transition states, in which the steric repulsion between the 3‐substituent of the cyclobutanone and the 3‐ and 3′‐substituents of the catalyst, as well as the entropy and solvent effects, are found to be critically important.     

Ethylene biosynthesis by 1-aminocyclopropane-1-carboxylic acid oxidase: a DFT study

The reaction catalyzed by the plant enzyme 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO) was investigated by using hybrid density functional theory. ACCO belongs to the non-heme iron(II) enzyme superfamily and carries out the bicarbonate-dependent two-electron oxidation of its substrate ACC (1-aminocyclopropane-1-carboxylic acid) concomitant with the reduction of dioxygen and oxidation of a reducing agent probably ascorbate. The reaction gives ethylene, CO(2), cyanide and two water molecules. A model including the mononuclear iron complex with ACC in the first coordination sphere was used to study the details of O-O bond cleavage and cyclopropane ring opening. Calculations imply that this unusual and complex reaction is triggered by a hydrogen atom abstraction step generating a radical on the amino nitrogen of ACC. Subsequently, cyclopropane ring opening followed by O-O bond heterolysis leads to a very reactive iron(IV)-oxo intermediate, which decomposes to ethylene and cyanoformate with very low energy barriers. The reaction is assisted by bicarbonate located in the second coordination sphere of the metal.