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.     

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.     

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.     

Highly Efficient Chemical Process To Convert Mucic Acid into Adipic Acid and DFT Studies of the Mechanism of the Rhenium‐Catalyzed Deoxydehydration

The production of bulk chemicals and fuels from renewable bio‐based feedstocks is of significant importance for the sustainability of human society. Adipic acid, as one of the most‐demanded drop‐in chemicals from a bioresource, is used primarily for the large‐volume production of nylon‐6,6 polyamide. It is highly desirable to develop sustainable and environmentally friendly processes for the production of adipic acid from renewable feedstocks. However, currently there is no suitable bio‐adipic acid synthesis process. Demonstrated herein is the highly efficient synthetic protocol for the conversion of mucic acid into adipic acid through the oxorhenium‐complex‐catalyzed deoxydehydration (DODH) reaction and subsequent Pt/C‐catalyzed transfer hydrogenation. Quantitative yields (99 %) were achieved for the conversion of mucic acid into muconic acid and adipic acid either in separate sequences or in a one‐step process.     

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.     

DFT Study of the Active Site of the XoxF‐Type Natural,Cerium‐Dependent Methanol Dehydrogenase Enzyme

Rare‐earth metal cations have recently been demonstrated to be essential co‐factors for the growth of the methanotrophic bacterium Methylacidiphilum fumariolicum SolV. A crystal structure of the rare‐earth‐dependent methanol dehydrogenase (MDH) includes a cerium cation in the active site. Herein, the Ce–MDH active site has been analyzed through DFT calculations. The results show the stability of the Ce^III–pyrroloquinoline quinone (PQQ) semiquinone configuration. Calculations on the active oxidized form of this complex indicate a 0.81 eV stabilization of the PQQ⁰ LUMO at cerium versus calcium, supporting the observation that the cerium cation in the active site confers a competitive advantage to Methylacidiphilum fumariolicum SolV. Using reported aqueous electrochemical data, a semi‐empirical correlation was established based on cerium(IV/III) redox potentials. The correlation allowed estimation of the cerium oxidation potential of +1.35 V versus saturated calomel electrode (SCE) in the active site. The results are expected to guide the design of functional model complexes and alcohol‐oxidation catalysts based on lanthanide complexes of biologically relevant quinones.     

DFT Study on the Recovery of Hoveyda–Grubbs‐Type Catalyst Precursors in Enyne and Diene Ring‐Closing Metathesis

DFT (B3LYP‐D) calculations have been used to better understand the origin of the recovered Hoveyda–Grubbs derivative catalysts after ring‐closing diene or enyne metathesis reactions. For that, we have considered the activation process of five different Hoveyda–Grubbs precursors in the reaction with models of usual diene and enyne reactants as well as the potential precursor regeneration through the release/return mechanism. The results show that, regardless of the nature of the initial precursor, the activation process needs to overcome relatively high energy barriers, which is in agreement with a relatively slow process. The precursor regeneration process is in all cases exergonic and it presents low energy barriers, particularly when compared to those of the activation process. This indicates that the precursor regeneration should always be feasible, unlike the moderate recoveries sometimes observed experimentally, which suggests that other competitive processes that hinder recovery should take place. Indeed, calculations presented in this work show that the reactions between the more abundant olefinic products and the active carbenes usually require lower energy barriers than those that regenerate the initial precatalyst, which could prevent precursor regeneration. On the other hand, varying the precursor concentration with time obtained from the computed energy barriers shows that, under the reaction conditions, the precursor activation is incomplete, thereby suggesting that the origin of the recovered catalyst probably arises from incomplete precursor activation.     

Does Silica Surface Catalyse Peptide Bond Formation? New Insights from First‐Principles Calculations

The role that silica surface could have played in prebiotic chemistry as a catalyst for peptide bond formation has been addressed at the B3LYP/6-31+G(d,p) level for a model reaction involving glycine and ammonia on a silica cluster mimicking an isolated terminal silanol group present at the silica surface. Hydrogen-bond complexation between glycine and the silanol is followed by the formation of the mixed surface anhydride Si(surf)-O-C(=O)-R, which has been suggested in the literature to activate the C=O bond towards nucleophilic attack by a second glycine molecule, here simulated by the simpler NH3 molecule. However, B3LYP/6-31+G(d,p) calculations show that formation of the surface mixed anhydride Si(surf)-O-C(=O)-R is disfavoured (delta(r)G298 approximately 6 kcal mol(-1)), and that the surface bond only moderately lowers the free-energy barrier of the nucleophilic attack responsible for peptide bond formation (deltaG298(double dagger) approximately 48 kcal mol(-1)) in comparison with the uncatalysed reaction (deltaG298(double dagger) approximately 52 kcal mol(-1)). A further decrease of the free-energy barrier of peptide bond formation (deltaG298(double dagger) approximately 41 kcal mol(-1)) is achieved by a single water molecule close to the reaction centre acting as a proton-transfer helper in the activated complex. A possible role of strained silica surface defects on the formation of the surface mixed anhydride Si(surf)-O-C(=O)-R has also been addressed.     

On the Mechanism of Bifunctional Squaramide‐Catalyzed Organocatalytic Michael Addition: A Protonated Catalyst as an Oxyanion Hole

A joint experimental–theoretical study of a bifunctional squaramide‐amine‐catalyzed Michael addition reaction between 1,3‐dioxo nucleophiles and nitrostyrene has been undertaken to gain insight into the nature of bifunctional organocatalytic activation. For this highly stereoselective reaction, three previously proposed mechanistic scenarios for the critical C?C bond‐formation step were examined. Accordingly, the formation of the major stereoisomeric products is most plausible by one of the bifunctional pathways that involve electrophile activation by the protonated amine group of the catalyst. However, some of the minor product isomers are also accessible through alternative reaction routes. Structural analysis of transition states points to the structural invariance of certain fragments of the transition state, such as the protonated catalyst and the anionic fragment of approaching reactants. Our topological analysis provides deeper insight and a more general understanding of bifunctional noncovalent organocatalysis.     

A DFT Study on the Mechanism of Rh2II,II‐Catalyzed Intramolecular Amidation of Carbamates

The potential‐energy surfaces of the reactions of dirhodium tetracarboxylate (Rh₂^II,II) catalyzed nitrene (NR) insertion into C H bonds were examined by a DFT computational study. A pure Becke exchange functional (B88) rather than a hybrid exchange functional (B3, BHandH) was found to be appropriate for the calculation of the energy difference between the singlet and triplet Rh₂^II,II–NH nitrene species. Rh₂^II,II–NR¹ (R¹=(S)‐2‐methyl‐1‐butylformyl) is thermodynamically more favorable with a free energy lower than that of Rh₂^II,II–N(PhI)R¹. The singlet and triplet states of Rh₂^II,II–NR¹ have similar stability. Singlet Rh₂^II,II–NR¹ undergoes a concerted NR insertion into the C H bond with simultaneous formation of the N H and N C bonds during C H bond cleavage; triplet Rh₂^II,II–NR¹ undergoes H atom abstraction to produce a diradical, followed by subsequent bond formation by diradical recombination. The singlet pathway is favored over the triplet in the context of the free energy of activation and leads to the retention of the chirality of the C atom in the NR insertion product. The reactivities of the C H bonds toward the nitrene‐insertion reaction follow the order tertiary>secondary>primary. Relative reaction rates were calculated for the six reaction pathways examined in this work.     

Ligand‐Exchange Processes on Solvated Zinc Cations: Water Exchange on [Zn(H2O)4(L)]2+⋅2 H2O (L=Heterocyclic Ligand)

The water‐exchange mechanisms of [Zn(H₂O)₄(L)]²⁺?2 H₂O (L=imidazole, pyrazole, 1,2,4‐triazole, pyridine, 4‐cyanopyridine, 4‐aminopyridine, 2‐azaphosphole, 2‐azafuran, 2‐azathiophene, and 2‐azaselenophene) have been investigated by DFT calculations (RB3LYP/6‐311+G**). The results support limiting associative reaction pathways that involve the formation of six‐coordinate intermediates [Zn(H₂O)₅(L)]²⁺?H₂O. The basicity of the coordinated heterocyclic ligands shows a good correlation with the activation barriers, structural parameters, and stability of the transition and intermediate states.     

Mechanism of the Tyrosine Ammonia Lyase Reaction—Tandem Nucleophilic and Electrophilic Enhancement by a Proton Transfer

Quantum mechanics/molecular mechanics calculations in tyrosine ammonia lyase (TAL) ruled out the hypothetical Friedel–Crafts (FC) route for ammonia elimination from L ‐tyrosine due to the high energy of FC intermediates. The calculated pathway from the zwitterionic L ‐tyrosine‐binding state (0.0 kcal mol^?1) to the product‐binding state ((E)‐coumarate+H₂N? MIO; ?24.0 kcal mol^?1; MIO=3,5‐dihydro‐5‐methylidene‐4H‐imidazol‐4‐one) involves an intermediate (IS, ?19.9 kcal mol^?1), which has a covalent bond between the N atom of the substrate and MIO, as well as two transition states (TS1 and TS2). TS1 (14.4 kcal mol^?1) corresponds to a proton transfer from the substrate to the N1 atom of MIO by Tyr300? OH. Thus, a tandem nucleophilic activation of the substrate and electrophilic activation of MIO happens. TS2 (5.2 kcal mol^?1) indicates a concerted C? N bond breaking of the N‐MIO intermediate and deprotonation of the pro‐S β position by Tyr60. Calculations elucidate the role of enzymic bases (Tyr60 and Tyr300) and other catalytically relevant residues (Asn203, Arg303, and Asn333, Asn435), which are fully conserved in the amino acid sequences and in 3D structures of all known MIO‐containing ammonia lyases and 2,3‐aminomutases.     

C−N Bond Formation from a Masked High‐Valent Copper Complex Stabilized by Redox Non‐Innocent Ligands

The reactivity of a stable copper(II) complex bearing fully oxidized iminobenzoquinone redox ligands towards nucleophiles is described. In sharp contrast with its genuine low‐valent counterpart bearing reduced ligands, this complex performs high‐yielding C?N bond formations. Mechanistic studies suggest that this behavior could stem from a mechanism akin to reductive elimination occurring at the metal center but facilitated by the ligand: it is proposed that a masked high oxidation state of the metal can be stabilized as a lower copper(II) oxidation state by the redox ligands without forfeiting its ability to behave as a high‐valent copper(III) center. These observations are substantiated by a combination of advanced EPR spectroscopy techniques with DFT studies. This work sheds light on the potential of redox ligands as promoters of unusual reactivities at metal centers and illustrates the concept of masked high‐valent metallic species.     

A QM/MM Investigation of the Catalytic Mechanism of Metal‐Ion‐Independent Core 2 β1,6‐N‐Acetylglucosaminyltransferase

β1,6‐GlcNAc‐transferase (C2GnT) is an important controlling factor of biological functions for many glycoproteins and its activity has been found to be altered in breast, colon, and lung cancer cells, in leukemia cells, in the lymhomonocytes of multiple sclerosis patients, leukocytes from diabetes patients, and in conditions causing an immune deficiency. The result of the action of C2GnT is the core 2 structure that is essential for the further elongation of the carbohydrate chains of O‐glycans. The catalytic mechanism of this metal‐ion‐independent glycosyltransferase is of paramount importance and is investigated here by using quantum mechanical (QM) (density functional theory (DFT))/molecular modeling (MM) methods with different levels of theory. The structural model of the reaction site used in this report is based on the crystal structures of C2GnT. The entire enzyme–substrate system was subdivided into two different subsystems: the QM subsystem containing 206 atoms and the MM region containing 5914 atoms. Three predefined reaction coordinates were employed to investigate the catalytic mechanism. The calculated potential energy surfaces discovered the existence of a concerted S_N2‐like mechanism. In this mechanism, a nucleophilic attack by O6 facilitated by proton transfer to the catalytic base and the separation of the leaving group all occur almost simultaneously. The transition state for the proposed reaction mechanism at the M06‐2X/6‐31G** (with diffuse functions on the O1′, O5′, O_Glu, and O6 atoms) level was located at C1? O6=1.74 Å and C1? O1=2.86 Å. The activation energy for this mechanism was estimated to be between 20 and 29 kcal mol^?1, depending on the method used. These calculations also identified a low‐barrier hydrogen bond between the nucleophile O6H and the catalytic base Glu320, and a hydrogen bond between the N‐acetamino group and the glycosidic oxygen of the donor in the TS. It is proposed that these interactions contribute to a stabilization of TS and participate in the catalytic mechanism.     

Lithium Choreography: Intramolecular Arylations of Carbamate‐Stabilised Carbanions and Their Mechanisms Probed by In Situ IR Spectroscopy and DFT Calculations

Deprotonation of O‐allyl, O‐propargyl or O‐benzyl carbamates in the presence of a lithium counterion leads to carbamate‐stabilised organolithium compounds that may be quenched with electrophiles. We now report that when the allylic, propargylic or benzylic carbamate bears an N‐aryl substituent, an aryl migration takes place, leading to stereochemical inversion and C‐arylation of the carbamate α to oxygen. The aryl migration is an intramolecular S_NAr reaction, despite the lack of anion‐stabilising aryl substituents. Our in situ IR studies reveal a number of intermediates along the rearrangement pathway, including a “pre‐lithiation complex,” the deprotonated carbamate, the rearranged anion, and the final arylated carbamate. No evidence was obtained for a dearomatised intermediate during the aryl migration. DFT calculations predict that during the reaction the solvated Li cation moves from the carbanion centre, thus freeing its lone pair for nucleophilic attack on the remote phenyl ring. This charge separation leads to several alternative conformations. The one having Li⁺ bound to the carbamate oxygen gives rise to the lowest‐energy transition structure, and also leads to inversion of the configuration. In agreement with the IR studies, the DFT calculations fail to locate a dearomatised intermediate.     

DFT Study of a 5‐endo‐trig‐Type Cyclization of 3‐Alkenoic Acids by Using Pd–Spiro‐bis(isoxazoline) as Catalyst: Importance of the Rigid Spiro Framework for Both Selectivity and Reactivity

The reaction pathway of an enantioselective 5‐endo‐trig‐type cyclization of 3‐alkenoic acids catalyzed by a chiral palladium–spiro‐bis(isoxazoline) complex, Pd–SPRIX, has been studied by density functional theory calculations. The most plausible pathway involves intramolecular nucleophilic attack of the carboxylate moiety on the C?C double bond activated by Pd–SPRIX and β‐H elimination from the resulting organopalladium intermediate. The enantioselectivity was determined in the cyclization step through the formation of a π‐olefin complex, in which one of the two enantiofaces of the olefin moiety was selected. The β‐H elimination occurs via a seven‐membered cyclic structure in which the acetate ligand plays a key role in lowering the activation barrier of the transition state. In the elimination step, the SPRIX ligand was found to behave as a monodentate ligand due to the hemilability of one of the isoxazoline units thereby facilitating the elimination. Natural population analysis of this pathway showed that the more weakly electron‐donating SPRIX ligand, compared with the bis(oxazoline) ligand, BOX, facilitated the formation of the π‐olefin complex intermediate, leading to a smaller overall activation energy and a higher reactivity of the Pd–SPRIX catalyst.     

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.     

Time‐Dependent Density Functional Theory Molecular Dynamics Simulations of Liquid Water Radiolysis

The early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water are investigated with time‐dependent density functional theory molecular dynamics (TD–DFT MD) simulations. Our aim is to verify that the double ionization of one target water molecule leads to the formation of atomic oxygen as a direct consequence of the Coulomb explosion of the molecule. To that end, we used TD–DFT MD simulations in which effective molecular orbitals are propagated in time. These molecular orbitals are constructed as a unitary transformation of maximally localized Wannier orbitals, and the ionization process was obtained by removing two electrons from the molecular orbitals with symmetry 1B₁, 3A₁, 1B₂ and 2A₁ in turn. We show that the doubly charged H₂O²⁺ molecule explodes into its three atomic fragments in less than 4 fs, which leads to the formation of one isolated oxygen atom whatever the ionized molecular orbital. This process is followed by the ultrafast transfer of an electron to the ionized molecule in the first femtosecond. A faster dissociation pattern can be observed when the electrons are removed from the molecular orbitals of the innermost shell. A Bader analysis of the charges carried by the molecules during the dissociation trajectories is also reported.