Ligand Displacement Reaction Paths in a Diiron Hydrogenase Active Site Model Complex

The mechanism and energetics of CO, 1‐hexene, and 1‐hexyne substitution from the complexes (SBenz)₂[Fe₂(CO)₆] (SBenz=SCH₂Ph) ( 1 ‐CO), (SBenz)₂[Fe₂(CO)₅(η²‐1‐hexene)] ( 1 ‐(η²‐1‐hexene)), and (SBenz)₂[Fe₂(CO)₅(η²‐1‐hexyne)] ( 1 ‐(η²‐1‐hexyne)) were studied by using time‐resolved infrared spectroscopy. Exchange of both CO and 1‐hexyne by P(OEt)₃ and pyridine, respectively, proceeds by a bimolecular mechanism. As similar activation enthalpies are obtained for both reactions, the rate‐determining step in both cases is assumed to be the rotation of the Fe(CO)₂L (L=CO or 1‐hexyne) unit to accommodate the incoming ligand. The kinetic profile for the displacement of 1‐hexene is quite different than that for the alkyne and, in this case, both reaction channels, that is, dissociative (S_N1) and associative (S_N2), were found to be competitive. Because DFT calculations predict similar binding enthalpies of alkene and alkyne to the iron center, the results indicate that the bimolecular pathway in the case of the alkyne is lower in free energy than that of the alkene. In complexes of this type, subtle changes in the departing ligand characteristics and the nature of the mercapto bridge can influence the exchange mechanism, such that more than one reaction pathway is available for ligand substitution. The difference between this and the analogous study of (μ‐pdt)[Fe(CO)₃]₂ (pdt=S(CH₂)₃S) underscores the unique characteristics of a three‐atom S?S linker in the active site of diiron hydrogenases.     

Mechanistic Insight into Peroxo‐Shunt Formation of Biomimetic Models for Compound II,Their Reactivity toward Organic Substrates,and the Influence of N‐Methylimidazole Axial Ligation

High‐valent iron‐oxo species have been invoked as reactive intermediates in catalytic cycles of heme and nonheme enzymes. The studies presented herein are devoted to the formation of compound II model complexes, with the application of a water soluble (TMPS)Fe^III(OH) porphyrin ([meso‐tetrakis(2,4,6‐trimethyl‐3‐sulfonatophenyl)porphinato]iron(III) hydroxide) and hydrogen peroxide as oxidant, and their reactivity toward selected organic substrates. The kinetics of the reaction of H₂O₂ with (TMPS)Fe^III(OH) was studied as a function of temperature and pressure. The negative values of the activation entropy and activation volume for the formation of (TMPS)Fe^IV?O(OH) point to the overall associative nature of the process. A pH‐dependence study on the formation of (TMPS)Fe^IV?O(OH) revealed a very high reactivity of OOH^? toward (TMPS)Fe^III(OH) in comparison to H₂O₂. The influence of N‐methylimidazole (N‐MeIm) ligation on both the formation of iron(IV)‐oxo species and their oxidising properties in the reactions with 4‐methoxybenzyl alcohol or 4‐methoxybenzaldehyde, was investigated in detail. Combined experimental and theoretical studies revealed that among the studied complexes, (TMPS)Fe^III(H₂O)(N‐MeIm) is highly reactive toward H₂O₂ to form the iron(IV)‐oxo species, (TMPS)Fe^IV?O(N‐MeIm). The latter species can also be formed in the reaction of (TMPS)Fe^III(N‐MeIm)₂ with H₂O₂ or in the direct reaction of (TMPS)Fe^IV?O(OH) with N‐MeIm. Interestingly, the kinetic studies involving substrate oxidation by (TMPS)Fe^IV?O(OH) and (TMPS)Fe^IV?O(N‐MeIm) do not display a pronounced effect of the N‐MeIm axial ligand on the reactivity of the compound II mimic in comparison to the OH^? substituted analogue. Similarly, DFT computations revealed that the presence of an axial ligand (OH^? or N‐MeIm) in the trans position to the oxo group in the iron(IV)‐oxo species does not significantly affect the activation barriers calculated for C?H dehydrogenation of the selected organic substrates.     

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.     

Structure and Functional Differences of Cysteine and 3-Mercaptopropionate Dioxygenases: A Computational Study

Thiol dioxygenases are important enzymes for human health; they are involved in the detoxification and catabolism of toxic thiol-containing natural products such as cysteine. As such, these enzymes have relevance to the development of Alzheimer's and Parkinson's diseases in the brain. Recent crystal structure coordinates of cysteine and 3-mercaptopropionate dioxygenase (CDO and MDO) showed major differences in the second-coordination spheres of the two enzymes. To understand the difference in activity between these two analogous enzymes, we created large, active-site cluster models. We show that CDO and MDO have different iron(III)-superoxo-bound structures due to differences in ligand coordination. Furthermore, our studies show that the differences in the second-coordination sphere and particularly the position of a positively charged Arg residue results in changes in substrate positioning, mobility and enzymatic turnover. Furthermore, the substrate scope of MDO is explored with cysteinate and 2-mercaptosuccinic acid and their reactivity is predicted.     

Theoretical investigation of the reaction mechanism of the dinuclear zinc enzyme dihydroorotase

The reaction mechanism of the dinuclear zinc enzyme dihydroorotase was investigated by using hybrid density functional theory. This enzyme catalyzes the reversible interconversion of dihydroorotate and carbamoyl aspartate. Two reaction mechanisms in which the important active site residue Asp250 was either protonated or unprotonated were considered. The calculations establish that Asp250 must be unprotonated for the reaction to take place. The bridging hydroxide is shown to be capable of performing nucleophilic attack on the substrate from its bridging position and the role of Zn(beta) is argued to be the stabilization of the tetrahedral intermediate and the transition state leading to it, thereby lowering the barrier for the nucleophilic attack. It is furthermore concluded that the rate-limiting step is the protonation of the amide nitrogen by Asp250 coupled with C-N bond cleavage, which is consistent with previous experimental findings from isotope labeling studies.     

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.     

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.     

Biodegradation of Herbicides by a Plant Nonheme Iron Dioxygenase: Mechanism and Selectivity of Substrate Analogues

Aryloxyalkanoate dioxygenases are unique herbicide biodegrading nonheme iron enzymes found in plants and hence, from environmental and agricultural point of view they are important and valuable. However, they often are substrate specific and little is known on the details of the mechanism and the substrate scope. To this end, we created enzyme models and calculate the mechanism for 2,4-dichlorophenoxyacetic acid biodegradation and 2-methyl substituted analogues by density functional theory. The work shows that the substrate binding is tight and positions the aliphatic group close to the metal center to enable a chemoselective reaction mechanism to form the C²-hydroxy products, whereas the aromatic hydroxylation barriers are well higher in energy. Subsequently, we investigated the metabolism of R- and S-methyl substituted inhibitors and show that these do not react as efficiently as 2,4-dichlorophenoxyacetic acid substrate due to stereochemical clashes in the active site and particularly for the R-isomer give high rebound barriers.     

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.     

Mechanism and exo-regioselectivity of organolanthanide-mediated intramolecular hydroamination/cyclization of 1,3-disubstituted aminoallenes: a computational study

The complete catalytic reaction course for the organolanthanide-assisted intramolecular hydroamination/cyclization (IHC) of 4,5-heptadien-1-ylamine by a prototypical [(eta(5)-Me5C5)2LuCH(SiMe3)2] precatalyst has been critically scrutinized by employing a reliable DFT method. A computationally verified mechanistic scenario for the IHC of 1,3-disubstituted aminoallene substrates has been proposed that is consistent with the empirical rate law determined by experiment and accounts for crucial experimental observations. It involves kinetically rapid substrate association and dissociation equilibria, facile and reversible intramolecular allenic C=C insertion into the Ln-N bond, and turnover-limiting protonation of the azacycle's tether functionality, with the amine-amidoallene-Ln adduct complex representing the catalyst's resting state. This mechanistic scenario bears resemblance to the mechanism that has been recently proposed in a computational exploration of aminodiene IHC. The unique features of the IHC of the two substrate classes are discussed. Furthermore, the thermodynamic and kinetic factors that control the regio- and stereoselectivity of aminoallene IHC have been elucidated. These achievements have provided a deeper insight into the catalytic structure-reactivity relationships in organolanthanide-assisted cyclohydroamination of unsaturated C-C functionalities.     

The preferred reaction path for the oxidation of methanol by PQQ-containing methanol dehydrogenase: addition-elimination versus hydride-transfer mechanism

The catalytic oxidation of methanol to formaldehyde by pyrroloquinoline quinone (PQQ)-containing methanol dehydrogenase (MDH) was investigated at density functional B3LYP level. The still controversial addition-elimination and hydride-transfer reaction mechanisms were analysed. Computations performed in the gas phase and in the protein environment indicated that both suggested reaction sequences involve very high activation barriers. In this situation, the reactions should have scarce probability to occur and the preference for one of the two paths cannot be stated. Here, we will show how some corrections to the successive steps in the addition-elimination mechanism can sensibly decrease the activation barriers height, making possible the determination of the MDH-preferred catalytic path.     

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.

     

Role of the variable active site residues in the function of thioredoxin family oxidoreductases

The enzymes of the thioredoxin family fulfill a wide range of physiological functions. Although they possess a similar CXYC active site motif, with identical environment and stereochemical properties, the redox potential and pK(a) of the cysteine pair varies widely across the family. As a consequence, each family member promotes oxidation or reduction reactions, or even isomerization reactions. The analysis of the three-dimensional structures gives no clues to identify the molecular source for the different active site properties. Therefore, we carried out a set of quantum mechanical calculations in active site models to gain more understanding on the elusive molecular-level origin of the differentiation of the properties across the family. The obtained results, together with earlier quantum mechanical calculations performed in our laboratories, gave rise to a consistent line of evidence, which points to the fact that both active site cysteines play an important role in the differentiation. In contrary to what was assumed, differentiation is not achieved through a different stabilization of the solvent exposed cysteine but, instead, through a fine tuning of the nucleophilicity of both active site cysteines. Reductant enzymes have both cysteine thiolates poorly stabilized, oxidant proteins have both cysteine thiolates highly stabilized, and isomerases have one thiolate (solvent exposed) poorly stabilized and the other (buried) thiolate highly stabilized. The feasibility of shifting the chemical equilibrium toward oxidation, reduction, or isomerization only through subtle electrostatic effects is quite unusual, and it relies on the inherent thermoneutrality of the catalytic steps carried out by a set of chemically equivalent entities all of which are cysteine thiolates. Such pattern of stabilization/destabilization, detected in our calculations is fully consistent with the observed physiological roles of this family of enzymes.     

H2 Activation in [FeFe]-Hydrogenase Cofactor Versus Diiron Dithiolate Models: Factors Underlying the Catalytic Success of Nature and Implications for an Improved Biomimicry

Catalytic H₂ oxidation has been dissected by means of DFT into the key steps common to the Fe₂ unit of both the [FeFe]-hydrogenase cofactor and selected biomimics. The aim was to elucidate the molecular details underlying the very different performances of the two systems. We found that the better enzyme performance is based on a single iron atom that is maintained electron-poor, favoring H₂ binding, although embedded within a highly electron-rich cofactor, ensuring a facile oxidation of the Fe₂–H₂ adduct. This is due to 1) CN⁻ coordinating to both iron atoms, due to their amphipathic Lewis acid/bas e properties, and 2) the 4Fe4S subunit further withdrawing electrons from the Fe₂ core. Preserving a moderate electron deficiency at a single iron also helps the cofactor preserve hydride affinity, which favors H₂ cleavage. Such valuable characteristics allow the biocatalyst to turnover close to equilibrium conditions. All previous biomimicry has shown, in contrast, the impossibility to properly balance the two apparently contrasting aforementioned requisites, although evident progress has been made by the H₂-ase community. Disclosure of the differences identified could inspire the design of novel biomimics, for instance, reconsidering the use of CN⁻ in the catalyst architecture. Indeed, in the presence of bases normally employed in oxidative catalysis, undesired stable protonation at coordinated CN⁻, which affects the opposite process (proton reduction), could be overcome.     

Mechanism of Alkyne Alkoxycarbonylation at a Pd Catalyst with P,N Hemilabile Ligands: A Density Functional Study

A detailed mechanism for alkyne alkoxycarbonylation mediated by a palladium catalyst has been characterised at the B3PW91‐D3/PCM level of density functional theory (including bulk solvation and dispersion corrections). This transformation, investigated via the methoxycarbonylation of propyne, involves a uniquely dual role for the P,N hemilabile ligand acting co‐catalytically as both an in situ base and proton relay coupled with a Pd⁰ centre, allowing for surmountable barriers (highest ΔG^≠ of 22.9 kcal mol^?1 for alcoholysis). This proton‐shuffle between methanol and coordinated propyne accounts for experimental requirements (high acid concentration) and reproduces observed regioselectivities as a function of ligand structure. A simple ligand modification is proposed, which is predicted to improve catalytic turnover by three orders of magnitude.     

Theoretical study of the full reaction mechanism of human soluble epoxide hydrolase

The complete reaction mechanism of soluble epoxide hydrolase (sEH) has been investigated by using the B3LYP density functional theory method. Epoxide hydrolases catalyze the conversion of epoxides to their corresponding vicinal diols. In our theoretical study, the sEH active site is represented by quantum-chemical models that are based on the X-ray crystal structure of human soluble epoxide hydrolase. The trans-substituted epoxide (1S,2S)-beta-methylstyrene oxide has been used as a substrate in the theoretical investigation of the sEH reaction mechanism. Both the alkylation and the hydrolytic half-reactions have been studied in detail. We present the energetics of the reaction mechanism as well as the optimized intermediates and transition-state structures. Full potential energy curves for the reactions involving nucleophilic attack at either the benzylic or the homo-benzylic carbon atom of (1S,2S)-beta-methylstyrene oxide have been computed. The regioselectivity of epoxide opening has been addressed for the two substrates (1S,2S)-beta-methylstyrene oxide and (S)-styrene oxide.     

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.     

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.